gene	protein	cdna	transcript	disease	vaf	tissue_source	sequencing_method	n_patients	age_range	anatomic_site	notes	primary_source	source_pmc	source_pmid	issva
PIK3CA	E109del	c.325_327delGAA	NM_006218.3	LM	n.r. (LEC line; Sanger, not quantified)	patient-derived cultured lymphatic endothelial cell line (Ly-LEC-2) from resected LM tissue, isolated via Folkman cell-sweeping; patient-matched fibroblasts (Ly-F-2) wild-type	Sanger sequencing of whole PIK3CA gene (after negative exon 8/10/21 screen); ABI 3500	1	pediatric	n.r.	novel in-frame 3-bp GAA deletion; LEC-specific mosaicism (fibroblast-negative); AKT-Ser473 hyperphosphorylated but no ERK hyperphosphorylation; relatively refractory to MK-2206	Blesinger 2018 PLoS ONE	PMC6037383	29985963	malformations/slow-flow/lm/isolated/lm
PIK3CA	E110del	c.328_330del	NM_006218.3	LM	1.06-2.70% (Brouillard); 14.3% (Li 2023, CVA293)	frozen resected lesion tissue (surgical leftover) (Brouillard); lesional tissue gDNA (Li 2023)	Ion AmpliSeq targeted PIK3CA 21-exon panel, ≥500x avg coverage on Ion PGM/Proton (Brouillard); deep exome + NGSure (Li 2023)	1 LM (+ 1 KTS in cohort) (Brouillard); 1 (Li 2023, CVA293)	n.r. (Brouillard); 11 y F (Li 2023)	Head&Neck/Trunk/Extremities (per-variant not resolved) (Brouillard); left upper thigh, GI and inguinal area (Li 2023)	non-hotspot ABD-domain variant; 3 lesional samples (VA-312/VA-339/VA-403) concordant (VAF 1.06/1.95/2.70%); mosaic; not targeted by the study hotspot ddPCR assay (covers only the 4 canonical hotspots); Li 2023 writes the same deletion as c.325_327del (alternative alignment within the GAG repeat; c.328_330del is the 3'-shifted HGVS form)	Brouillard 2021 Orphanet J Rare Dis; Li 2023 Nat Med	PMC8194016; PMC11184491	34112235; 37264205	malformations/slow-flow/lm/isolated/lm
PIK3CA	R88Q	c.263G>A	NM_006218.3	LM	0.52%	FFPE (archived block/slides)	UMI-based 49-gene panel (~86,570x raw / ~1,892x effective) on Illumina NovaSeq; BDA qPCR + Sanger validation	1 (CVA183)	17 y (F; CVA183)	pelvis (CVA183)	low-VAF FFPE-derived call within reported FFPE VAF range 0.52-31.5% (median 6.25%, n=22); non-hotspot PIK3CA	Li 2023 Nat Med	PMC11184491	37264205	malformations/slow-flow/lm/isolated/lm
PIK3CA	R88Q	c.263G>A	NM_006218.3	GLA	1.30%	FFPE tissue gDNA (CVA211)	UMI-based 49-gene panel (ultra-deep, ~1,892x effective); NOT orthogonally validated (insufficient residual DNA), accepted on recurrent-hotspot basis	1 of 4 GLA patients with a pathogenic variant (genes differ: PIK3CA/BRAF/HRAS/KRAS); only PIK3CA case	13 y (M; CVA211)	GLA phenotype (bone/organ lymphatic malformations)	"main text (verbatim): ""Four participants with GLA were confirmed to have a pathogenic variant, and all had a very low VAF ranging from 0.21% to 1.3%"" (gene not named; only 1 of the 4 is PIK3CA)"	Li 2023 Nat Med	PMC11184491	37264205	malformations/slow-flow/lm/complex/gla
PIK3CA	N345K	c.1035T>A	NM_006218.3	LM	<=1.4%	lesion biopsy (7 lesion cores + skin + salivary gland; LR18-536)	VANseq 44-gene targeted deep-sequencing panel + ddPCR confirmation	1	2y (0-5y)	isolated LM; multi-lesion sampled	non-hotspot missed by initial hotspot-ddPCR screen; VAF variable across lesion samples (undetectable to 1.4%); low-level positive in skin (0.3%); salivary gland negative; interpreted as pathogenic	Zenner 2022 HGG Adv	PMC8972000	35373151	malformations/slow-flow/lm/isolated/lm
PIK3CA	C420R	c.1258T>C	NM_006218.3	LM	LEC line (monoallelic in vitro) (Blesinger); 0.22% (Li 2023, CVA199)	patient-derived cultured LEC line (Ly-LEC-1) from resected LM tissue; patient-matched fibroblasts (Ly-F-1) wild-type (Blesinger); lesional tissue gDNA (Li 2023)	Sanger sequencing of PIK3CA exons 8/10/21 (Blesinger); UMI panel + NGSure (Li 2023)	1 (Blesinger); 1 (Li 2023, CVA199)	pediatric (Blesinger); 7 y M (Li 2023)	n.r. (Blesinger); tongue and airway (Li 2023)	cell-type specificity to LECs; AKT and ERK hyperphosphorylation; MK-2206 sensitive; LEC line (Ly-LEC-1/LEC-A) originally established by Norgall et al. 2007 BMC Cancer (PMID 17584927), not Osborn/Dickie	Blesinger 2018 PLoS ONE; Li 2023 Nat Med	PMC6037383; PMC11184491	29985963; 37264205	malformations/slow-flow/lm/isolated/lm
PIK3CA	E542K	c.1624G>A	NM_006218.3	LM	1-11% (Brouillard 2021: 1.11-8.17%, 11% LM tissue; Li 2023: 1-7.04%; Osborn 2015: n.r.)	frozen resected lesion tissue; primary LEC isolation in 1 LM (CD31+/CD34- LEC fraction VAF 32%) (Brouillard); lesional tissue gDNA, FFPE gDNA, cfDNA from LM fluid (CVA323) (Li 2023); LEC cultures from LM tissue or fluid (Osborn 2015)	Ion AmpliSeq PIK3CA panel + hotspot ddPCR (Bio-Rad, ≥5 SPD in ≥10,000 droplets, 30 ng input) (Brouillard); amplicon panel, ultra-deep exome 1611-1637x, UMI panel (Li 2023); direct sequencing of cultured LECs (Osborn 2015)	26 LM (+ 3 LVM, 1 CLVM, 1 PROS in cohort) (Brouillard); 6 (Li 2023); n.r. (Osborn 2015: E542K or E545A in lesion-derived LECs of 4 patients)	n.r. (Brouillard); 8 months-15 y (Li 2023)	Head&Neck/Trunk/Extremities (Brouillard); axilla/upper arm, flank, hand/finger, neck, face/chin (Li 2023)	helical-domain hotspot; strong LEC enrichment (32% vs bulk 11%); mosaic; multi-sample concordance; Osborn 2015 abstract-level (somatic status not explicitly stated for cultured LECs); VAF detail: Brouillard Table 4 per-sample 1.11-8.17% (VA-364, VA-50, VA-868), Table 2 LM tissue 11%, all-LM PIK3CA range 0.54-11.34% (Table 1); Li 2023 CVA32 1%, CVA149 2%, CVA133 1.7%, CVA218 7.04%, CVA323 2.17%, CVA329 1.23%	Brouillard 2021 Orphanet J Rare Dis; Li 2023 Nat Med; Osborn 2015 Hum Mol Genet	PMC8194016; PMC11184491	34112235; 37264205; 25292196	malformations/slow-flow/lm/isolated/lm
PIK3CA	E542K	c.1624G>A	NM_006218.3	GLA	1.1-3.5% (LM tissue); 33.7% in isolated LM-LECs	LM biopsy (fresh, surgical) + paired blood (GLA051, GLA061; both blood-negative); LM-LECs isolated by MACS (CD31+/podoplanin+) from GLA061 only (the GLA054 FACS-LEC sample carries Q546K, a different variant)	two-tier NGS Illumina NextSeq 500: hybrid-capture 1370-gene discovery panel (510x) + amplicon PIK3CA panel (13,819x); Sanger (>15% VAF)/pyrosequencing (5-15%)/ddPCR (<5%) confirmation	2 GLA (GLA051, GLA061)	16 y and 35 y (GLA061, GLA051)	GLA051: retroperitoneal + right-thigh mixed LM, chylous ascites, kidney compression (nephrectomy), no osteolysis; GLA061: cervicofacial + thoracic complex LM with cervical/cranial lymphatic-venous + intracranial venous malformations, no osteolysis	blood-negative; LM-tissue VAF 1.1-23%; LM-LEC VAF 28-33%; paper reports variants against NM_006218.2 (coding positions identical to NM_006218.3 used here)	Rodriguez-Laguna 2019 J Exp Med	PMC6363432	30591517	malformations/slow-flow/lm/complex/gla
PIK3CA	E545A	c.1634A>C	NM_006218.3	LM	n.r. (LEC line; direct sequencing)	lesion-derived cultured LECs (CD31/podoplanin sorted; per abstract)	direct sequencing (per abstract)	1	n.r.	n.r.	Osborn 2015 (PMID 25292196) paywalled, no PMC; abstract-only read 2026-10-09: LECs isolated by CD31/podoplanin sorting from 5 unrelated LM lesions, E542K and E545A found in lesion-derived cells of 4 patients by direct sequencing	Osborn 2015 Hum Mol Genet	n.r.	25292196	malformations/slow-flow/lm/isolated/lm
PIK3CA	E545G	c.1634A>G	NM_006218.3	LM	6.55-10.01%	frozen resected lesion tissue	Ion AmpliSeq PIK3CA panel (≥500x)	1 (only LM patient with this variant)	n.r.	n.r. (VA-10)	rare non-canonical helical variant at hotspot codon; two samples from VA-10 both concordant	Brouillard 2021 Orphanet J Rare Dis	PMC8194016	34112235	malformations/slow-flow/lm/isolated/lm
PIK3CA	E545K	c.1633G>A	NM_006218.3	LM	0.2-10.6% (Brouillard 2021: 1.73-7.32%; Zenner 2022: 0.7-10.6%; Wang 2021: 6.06%; Li 2023: 0.2-10.62%; Blesinger 2018: LEC lines)	frozen resected lesion tissue (Brouillard); lesion biopsy (Zenner 2022); surgically resected lymphatic tissue, peripheral blood as germline control (Wang 2021); lesional tissue gDNA, FFPE gDNA, cfDNA from LM fluid (Li 2023); cultured LEC lines Ly-LEC-12 and Ly-LEC-17, matched fibroblasts wild-type (Blesinger 2018)	Ion AmpliSeq PIK3CA panel + hotspot ddPCR (Brouillard); VANseq + ddPCR (Zenner 2022); Illumina HiSeq X10 WES (Agilent SureSelectXT2) + Bio-Rad QX200 ddPCR validation (Wang 2021); deep exome, UMI panel, NGSure / repeat UMI run (Li 2023); Sanger exons 8/10/21 (Blesinger 2018)	27 LM + 7 non-LM E545K carriers (subtype split not fully recoverable from Table 1 aggregate; includes >=1 CLOVES, VA-1158-T) (Brouillard); 2 (Zenner 2022); 1 of 6 (Wang 2021, patient 740368); 8 (Li 2023); 2 (Blesinger 2018)	n.r. (Brouillard); 2-3 y (Zenner 2022); 25 mo M (Wang 2021); 3 weeks-16 y (Li 2023); infant + adult (Blesinger 2018)	Head&Neck/Trunk/Extremities (Brouillard); isolated LM (Zenner 2022); left neck microcystic LM with bilateral parapharyngeal, retropharyngeal and prevertebral extension and airway obstruction (Wang 2021); neck, cheek, tongue, thigh, axilla/chest wall, face (Li 2023)	most common LM variant; VAF variable across multi-sample (VA-528: 4.3/6.24/7.32/1.87%); Zenner 2022 re-identified in 2 previously ddPCR-negative patients (2-3y, isolated LM); VAF detail: Brouillard Table 4 per-sample 1.73-7.32% (VA-528 4.3/6.24/7.32/1.87, VA-869 4.0/1.73), all-LM PIK3CA range 0.54-11.34% (Table 1); Zenner 2022 VANseq 0.7-10.6%, ddPCR 0.5-4.8%; Wang 2021 WES 6.06% (4/66 reads), ddPCR 2.14% (6/281); Li 2023 CVA07 7%, CVA16 9%, CVA51 3%, CVA150 3.2%, CVA208 6%, CVA212 1.33%, CVA262 10.62%, CVA286 0.2%	Brouillard 2021; Zenner 2022; Wang 2021 Orphanet J Rare Dis; Li 2023 Nat Med; Blesinger 2018 PLoS ONE	PMC8194016; PMC8972000; PMC8106842; PMC11184491; PMC6037383	34112235; 35373151; 33964933; 37264205; 29985963	malformations/slow-flow/lm/isolated/lm
PIK3CA	E545K	c.1633G>A	NM_006218.3	KLA	11.30%	abdominal mass tissue biopsy (gDNA); atypical KLA (spindled-to-round cells, D2-40+/PROX1+ lymphatic channels)	deep exome sequencing at 249x; confirmed on follow-up clinical testing	1 (CVA221)	20y male	mesentery, retroperitoneum, presacral area, pelvis, mediastinum; cystic lesions in pelvic bones/spine/spleen	switched from sirolimus to alpelisib after diagnosis; improved on 125 mg/day	Li 2023 Nat Med	PMC11184491	37264205	malformations/slow-flow/lm/complex/kla
PIK3CA	Q546K	c.1636C>A	NM_006218.3	LM	n.r. (LEC line; Sanger, not quantified)	patient-derived cultured LEC line (Ly-LEC-10) from resected LM tissue; patient-matched fibroblasts (Ly-F-10) wild-type	Sanger sequencing of PIK3CA exons 8/10/21	1	pediatric	n.r.	novel non-hotspot activating variant; documented in ovarian/glioblastoma tumors but first in LECs; AKT-Ser473 and ERK hyperphosphorylation	Blesinger 2018 PLoS ONE	PMC6037383	29985963	malformations/slow-flow/lm/isolated/lm
PIK3CA	Q546K	c.1636C>A	NM_006218.3	GLA	3.1-3.4% (LM tissue); 27.9% in isolated LM-LECs	LM biopsy (GLA054-LM; surgical, no FFPE annotation) + isolated LM-LECs (FACS: CD31+/podoplanin+/CD34low, from fresh tissue) + paired blood	two-tier NGS as above (hybrid-capture + amplicon 13,819x)	1 GLA patient	38 y (F; GLA054)	LM of left upper limb + hemithorax (microcystic-predominant), congenital; no osteolysis, no visceral involvement; hemothorax effusion (GLA054)	non-hotspot helical variant; blood-negative mosaic; first report of Q546K in GLA; paper reports variants against NM_006218.2 (coding positions identical to NM_006218.3 used here)	Rodriguez-Laguna 2019 J Exp Med	PMC6363432	30591517	malformations/slow-flow/lm/complex/gla
PIK3CA	Q546R	c.1637A>G	NM_006218.3	LM	2.16-3.96%	frozen resected lesion tissue	Ion AmpliSeq PIK3CA panel	1 (only patient with Q546R in LM cohort)	n.r.	n.r. (VA-886)	helical-domain variant (not on standard ddPCR panel); two samples from VA-886 concordant	Brouillard 2021 Orphanet J Rare Dis	PMC8194016	34112235	malformations/slow-flow/lm/isolated/lm
PIK3CA	M1043I	c.3129G>A	NM_006218.3	CCLA	5.60%	rectal wall tissue biopsy (gDNA)	deep exome sequencing (~400-470x)	1 (CVA65)	9y female	extensive abdominal-pelvic LM with chylorrhea from rectum/vagina; leaks into sigmoid colon and vaginal vault on DCMRL	3y history protein-losing enteropathy; sirolimus discontinued for AEs; alpelisib 100 mg/day initiated, well-tolerated, DCMRL improved	Li 2023 Nat Med	PMC11184491	37264205	malformations/slow-flow/lm/complex/ccla
PIK3CA	H1047L	c.3140A>T	NM_006218.3	LM	2.47-6.91% (Brouillard 2021: 2.47-2.52%; Li 2023: 5-6.91%; Blesinger 2018 LEC line, Osborn 2015: n.r.)	frozen resected lesion tissue (Brouillard); lesional tissue gDNA (CVA27), FFPE gDNA (CVA78) (Li 2023); cultured LEC line Ly-LEC-14, matched fibroblasts wild-type (Blesinger 2018); LEC culture from the LM lesion of a patient previously diagnosed with CLOVES (Osborn 2015)	Ion AmpliSeq PIK3CA panel (NGS; VA-230 reported values are NGS averages, not ddPCR) (Brouillard); deep exome (CVA27), UMI panel (CVA78) (Li 2023); Sanger exons 8/10/21 (Blesinger 2018); direct sequencing (Osborn 2015)	3 LM (Brouillard); 2 (Li 2023); 1 (Blesinger 2018); 1 (Osborn 2015)	n.r. (Brouillard); 11 y, 14 y (Li 2023); adult (Blesinger 2018)	n.r. (VA-230, Brouillard); face and tongue (microcystic), left upper arm and axilla (Li 2023)	kinase-domain hotspot; low VAF; two samples from VA-230 concordant; Osborn 2015 case previously diagnosed with CLOVES (abstract-level); VAF detail: Brouillard VA-230 NGS 2.47-2.52%; Li 2023 CVA27 5%, CVA78 6.91%	Brouillard 2021 Orphanet J Rare Dis; Li 2023 Nat Med; Blesinger 2018 PLoS ONE; Osborn 2015 Hum Mol Genet	PMC8194016; PMC11184491; PMC6037383	34112235; 37264205; 29985963; 25292196	malformations/slow-flow/lm/isolated/lm
PIK3CA	H1047L	c.3140A>T	NM_006218.3	GLA	18.5% (LM tissue, FFPE; GLA006)	LM biopsy (fresh + FFPE) + paired blood	two-tier NGS as above (13,819x amplicon)	1 GLA patient	23 y (M; GLA006)	multifocal LM with bone involvement	kinase hotspot; blood-negative mosaic; paper reports variants against NM_006218.2 (coding positions identical to NM_006218.3 used here)	Rodriguez-Laguna 2019 J Exp Med	PMC6363432	30591517	malformations/slow-flow/lm/complex/gla
PIK3CA	H1047L	c.3140A>T	NM_006218.3	CCLA	0.15-1.25%	CD31+ cells enriched from pleural fluid at lymphangiogram (CLA059); gDNA fluid (CLA092, CLA088)	amplicon-based 35-gene panel + UMI-based 49-gene panel (ultra-deep); BDA qPCR + Sanger	3 (CLA059 0.68%, CLA092 1.25%, CLA088 0.15%)	pediatric	CCLA with pleural/pericardial effusions, ascites, constrictive pericarditis, PLE, anasarca	second hotspot PIK3CA variant co-occurring with H1047R in same participant (CLA059); dual PIK3CA hotspot call	Li 2023 Nat Med	PMC11184491	37264205	malformations/slow-flow/lm/complex/ccla
PIK3CA	H1047R	c.3140A>G	NM_006218.3	LM	2.33-10.99% (Brouillard 2021: 2.33-10.99%; Li 2023: 2.97-6.7%; Zenner 2022: n.r.)	frozen resected lesional tissue (Brouillard); lesional tissue gDNA, FFPE (CVA39) (Li 2023); lesion biopsy (Zenner 2022)	Ion AmpliSeq PIK3CA panel + hotspot ddPCR (Brouillard); deep exome, UMI panel (Li 2023); ddPCR hotspot panel only (Zenner 2022 screening cohort; not among the VANseq-confirmed variants)	17 LM (Brouillard, Table 1); 6 (Li 2023); 1 (Zenner 2022 Table 2 tally)	n.r. (Brouillard); 17 months-23 y (Li 2023)	Head&Neck/Trunk/Extremities (Brouillard, cohort level); chest, elbow, face/orbit, neck, retropharynx (Li 2023); isolated LM (Zenner 2022)	kinase-domain hotspot; third most frequent LM variant in Brouillard 2021 (17 of 74 LM hotspot calls); Zenner 2022 Table 2 tally case used as histology/IHC comparator (VE1 IHC-negative) vs BRAF-mutant LM; VAF detail: Li 2023 CVA39 3.2%, CVA151 4.3%, CVA167 6.1%, CVA222 5.3%, CVA234 6.7%, CVA320 2.97%	Brouillard 2021 Orphanet J Rare Dis; Li 2023 Nat Med; Zenner 2022 HGG Adv	PMC8194016; PMC11184491; PMC8972000	34112235; 37264205; 35373151	malformations/slow-flow/lm/isolated/lm
PIK3CA	H1047R	c.3140A>G	NM_006218.3	GLA	23.0% (LM tissue, FFPE; GLA002)	LM (FFPE) from GLA002 (sole H1047R case); iliac/sacral bone + fascia from same patient screened (background reads only); paired blood negative	two-tier NGS as above (13,819x amplicon); Sanger/pyrosequencing/ddPCR confirmation	1 GLA (GLA002)	17 y (GLA002)	pelvic LM (lumbosacral spine, gluteal region); axial + appendicular osteolysis (iliac bones, sacro-coccygeal vertebrae, L5) with lower-limb paraplegia (GLA002)	kinase hotspot; GLA002 bulk LM VAF 23.0% (FFPE); Prox1-CreERT2;LSL-Pik3ca^H1047R mouse model recapitulates lymphatic hyperplasia and rapamycin-responsive dysfunction; paper reports variants against NM_006218.2 (coding positions identical to NM_006218.3 used here)	Rodriguez-Laguna 2019 J Exp Med	PMC6363432	30591517	malformations/slow-flow/lm/complex/gla
PIK3CA	H1047R	c.3140A>G	NM_006218.3	KLA	0.41%	cfDNA plasma (CVA52)	UMI-based 49-gene panel (ultra-deep, 8-bp UMIs); BDA qPCR + Sanger validation	1 (CVA52)	12 y (CVA52)	mediastinal LM with skull, liver and splenic lesions (diffuse; CVA52, atypical KLA)	sub-1% VAF; one of 24 participants with P/LP variants at VAF <=1% requiring UMI error correction	Li 2023 Nat Med	PMC11184491	37264205	malformations/slow-flow/lm/complex/kla
PIK3CA	H1047R	c.3140A>G	NM_006218.3	CCLA	0.89%	CD31+ cells enriched from pleural fluid collected at lymphangiogram	amplicon-based 35-gene panel + UMI-based 49-gene panel (dual confirmation); BDA qPCR + Sanger	1 (CLA059; text reports 0.89%)	pediatric	CCLA with pleural effusions, pericardial effusion, ascites, constrictive pericarditis, LE edema, PLE, anasarca	co-occurring with PIK3CA H1047L in same sample (dual hotspot); expanded genetic landscape - PIK3CA in CCLA	Li 2023 Nat Med	PMC11184491	37264205	malformations/slow-flow/lm/complex/ccla
PIK3CD	L666P	c.1997T>C	NM_005026.4	LM	2% (WES 5/289 reads); 3% (ddPCR 2/71 droplets)	peripheral blood (germline) + surgically resected lymphatic tissue from head-and-neck LM (Beijing Children's Hospital)	Illumina HiSeq X10 WES with Agilent SureSelectXT2 Target Enrichment; BWA/GATK/ANNOVAR; digital PCR validation; mean coverage 142x blood / 166x tissue	1 (patient 739889 of 6 LM cohort; patient 740368 had PIK3CA E545K instead)	2 months, male	left neck macrocystic LM, 3.7 x 6.5 x 6.3 cm, left parapharyngeal + retropharyngeal spaces, airway obstruction	novel variant, first report of PIK3CD in LM; L666P in PIK helical domain; HUVEC functional studies showed increased proliferation/migration and mTOR hyperactivation; PMC8106842 correctly attributed to Wang 2021 (not Rodriguez-Laguna 2019)	Wang 2021 Orphanet J Rare Dis	PMC8106842	33964933	malformations/slow-flow/lm/isolated/lm
NRAS	Q61R	c.182A>G	NM_002524.4	KLA	Barclay 2019: 1-28%; Li 2023: 0.54-5.1%; Brown 2026: 4.69% (pleural-fluid cfDNA)	FFPE lesional tumor tissue (biopsy 2/5 or autopsy 3/5) + uninvolved control tissue in 3/5 (Barclay); plasma cfDNA (CVA313, CVA14, CLA164) and FFPE gDNA (CVA177) (Li 2023); pleural-fluid cfDNA, no histology (Brown 2026)	Illumina HiSeq 2500 WES with SureSelectXT Human All Exon V5; GATK4/Mutect2 with panel-of-normals; TaqMan digital PCR validation (QuantStudio 3D chip v2, assay C_44193858_10); one sample also targeted high-throughput panel (Barclay); UMI-based 49-gene panel (Li 2023); pleural-fluid cfDNA, targeted 51-gene vascular malformation panel at CHOP (Brown 2026)	10 KLA (Barclay); 4 additional (Li 2023): CVA313, CVA177, CVA14, CLA164; 1 (Brown 2026)	Barclay 2019: 1-30 y at diagnosis (positive patients; median not stated); KLA typically pediatric/early adulthood; 4 y F (Brown 2026)	thoracic/mediastinal, pleural, pulmonary, retroperitoneum, spleen, cutaneous/subcutaneous (trunk/thigh/perineum), axilla, bone/vertebrae (Barclay); CVA14: chylothorax, sclerotic vertebral lesions, mediastinal lymphatic enhancement (Li 2023); refractory pleural + pericardial chylous effusions, diffuse thoracic/abdominal lymphatic abnormality on MR lymphangiography (Brown 2026)	CVA14 sample drawn prior to trametinib start; changed from sirolimus to trametinib; D-dimer dropped from 37 to <5 mg/L FEU by cycle 2, pleural effusions resolved; Brown 2026: presumed KLA diagnosed on clinical/radiologic/cfDNA grounds, sirolimus insufficient, trametinib resolved effusions within 7 weeks	Barclay 2019 Genet Med; Li 2023 Nat Med; Brown 2026 Case Rep Pediatr	PMC6565516; PMC11184491; PMC13501887	30542204; 37264205; 42639465	malformations/slow-flow/lm/complex/kla
NRAS	Q61R	c.182A>G	NM_002524.4	GLA	30%	lymphangiomatosis endothelial cells (LyECs) isolated from GLA-affected tissue	whole-exome sequencing (WES)	1 (single-patient case report)	n.r.	n.r.	Paper PMID29397482 = Manevitz-Mendelson E et al 2018 Angiogenesis 21(2):287-298 (GLA case with NRAS Q61R); cited by Barclay 2019; paywalled (no PMC); abstract-only read 2026-10-09 (WES of LyECs from GLA tissue, single patient; protein change, VAF and clinical detail taken from the Barclay 2019 citation)	Manevitz-Mendelson 2018 Angiogenesis	n.r.	29397482	malformations/slow-flow/lm/complex/gla
NRAS	Q61K	c.181C>A	NM_002524.4	KLA (cellular)	n.r.	n.r. (abstract only; series biopsies: skin, soft tissue, bone, spleen)	n.r.	1 (2 specimens)	n.r.	n.r.	Allen-Rhoades et al. 2022 Hum Pathol (PMID 35202617); paywalled (no PMC); abstract-only read 2026-10-09: series of 3 cellular-KLA patients (ages 2 y, 2 mo, 4 y; biopsies of skin, soft tissue, bone, spleen), variant-to-patient linkage not given in the abstract	Allen-Rhoades et al. 2022 Hum Pathol (PMID 35202617)	n.r.	35202617	malformations/slow-flow/lm/complex/kla
NRAS	Q61R	c.182A>G	NM_002524.4	CCLA	n.r.	lesional specimen (abstract only; full text paywalled)	n.r.	1	n.r.	central conducting lymphatics	First report of NRAS Q61R in CCLA (Yang 2026 Hum Mol Genet, DOI 10.1093/hmg/ddag070). Same paper reports a PPFIBP1::ROS1 fusion localized to D2-40+ lymphatic endothelium in a GSD patient; fusions are outside this point-variant table. Abstract-only read 2026-10-09 (paywalled, no PMC).	Yang 2026 Hum Mol Genet	n.r.	42544506	malformations/slow-flow/lm/complex/ccla
HRAS	A59_Q61delinsGGSIL	c.176_182delinsGAGGATCCATACT	NM_005343.4	KLA (cellular)	n.r.	biopsies (skin, soft tissue, bone, spleen; series-level, not linked to this patient)	n.r.	1 (of 3 cellular-KLA patients in the series)	n.r.	n.r.	Allen-Rhoades et al. 2022 Hum Pathol (PMID 35202617); paywalled (no PMC); abstract-only read 2026-10-09: series of 3 cellular-KLA patients (ages 2 y, 2 mo, 4 y; biopsies of skin, soft tissue, bone, spleen), variant-to-patient linkage not given in the abstract	Allen-Rhoades et al. 2022 Hum Pathol (PMID 35202617)	n.r.	35202617	malformations/slow-flow/lm/complex/kla
HRAS	E63_S65delinsDIPP	c.189_195delinsCATCCCGCCG	NM_005343.4	KLA	0.54%	tissue (gDNA; CVA102)	UMI-based 49-gene panel (ultra-deep)	1 (CVA102)	40 y (CVA102)	diffuse-appearing lesions on imaging (no specific site named; CVA102)	novel HRAS variant (this specific mutation not previously described); HRAS was already a known KLA driver	Li 2023 Nat Med	PMC11184491	37264205	malformations/slow-flow/lm/complex/kla
HRAS	M72_R73insHSAMRDQYM	c.191_217dup	NM_005343.4	GLA	0.51-0.63%	cfDNA from lymphatic (chylous) fluid	UMI-based 49-gene panel sequencing on cfDNA	1 (CVA09)	40y	pelvis with cutaneous microcysts; chylous effusions and chylous ascites requiring frequent paracenteses/thoracenteses	novel HRAS 27-bp in-frame duplication; novel genotype-phenotype association; confirmed by repeat UMI sequencing (this specific variant was not itself functionally assayed)	Li 2023 Nat Med	PMC11184491	37264205	malformations/slow-flow/lm/complex/gla
KRAS	G12D	c.35G>A	NM_004985.5	CCLA	1.4-44%	CD31+ endothelial cells enriched from lymphatic fluid (CLA149 at 44%); nevus sebaceous skin biopsy (Sheppard Individual 1 at 23%); tissue/fluid gDNA for others	amplicon-based 35-gene panel (CLA149 + CLA062; Li 2023); Nevus Gene Set targeted panel, Genomics and Pathology Services, WashU (Sheppard Individual 1)	>=2 (CLA149; Sheppard Individual 1)	CLA149 = 16 y, CLA062 = 6 months (Li 2023); Sheppard Individual 1 = infant male, born 33w+4d premature, died 7 months	CLA149: CCLA; Sheppard Individual 1: NSS+ECCL hybrid, renal hilum, retroperitoneum, mesentery, left pleural cavity, mediastinum, perihilar/pulmonary + supraclavicular/neck	high-VAF (44%) attributed to CD31+ enrichment (endothelial-carried variant); Sheppard case leukocyte-negative (blood-negative mosaic) tissue-restricted to nevus sebaceous	Li 2023 Nat Med; Sheppard 2023 JCI Insight	PMC11184491; PMC10243805	37264205; 37154160	malformations/slow-flow/lm/complex/ccla
KRAS	G12D	c.35G>A	NM_004985.5	KLA	0.55%	cfDNA isolated from blood (0.55%) and lymphatic fluid (0.39%)	ultra-deep UMI-based 49-gene panel	1 (CLA201)	23 y (CLA201)	KLA	dual-sample confirmation (blood cfDNA 0.55%, fluid cfDNA 0.39%); novel KRAS G12D in KLA	Li 2023 Nat Med	PMC11184491	37264205	malformations/slow-flow/lm/complex/kla
KRAS	G12V	c.35G>T	NM_004985.5	GSD	23% (targeted panel, 142/620 reads); 28% (WES, 15/55 reads)	fresh-frozen bone tissue from resected humerus with intraosseous lymphatics (transhumeral amputation at 36y); paired peripheral blood germline control	Ion Torrent 408-gene Ion AmpliSeq Comprehensive Cancer Panel on Ion Proton, median >2000x; confirmatory Illumina WES with Agilent SureSelect v6, median 256x tissue / 73x blood; Mutect2 somatic calling	1 (index GSD patient)	pathologic humeral fractures at 6y and 8y; chronic ascites/exudative enteropathy by 33y; amputation at 36y; death from sepsis at 37y	multifocal osteolysis: right clavicle, humerus, radius, cubitus, right femur, tibia, D10 vertebra; also chronic ascites with intestinal lymphangiectasias	no additional somatic/germline mutations; PIK3CA and NRAS negative; no CNVs; companion iLEC-Kras mouse model confirmed pathogenicity and trametinib responsiveness	Homayun-Sepehr 2021 JCI Insight	PMC8410066	34156985	malformations/slow-flow/lm/complex/gsd
KRAS	G12V	c.35G>T	NM_004985.5	CCLA	0.77% (Li 2023, CLA063); 29% (Sheppard 2023, nevus sebaceous)	gDNA fluid (lymphatic/chylous; CLA063) (Li 2023); nevus sebaceous scalp biopsy, absent in blood (Sheppard 2023)	UMI-based 49-gene panel (ultra-deep, error-corrected) (Li 2023); clinical gene panel (Sheppard 2023)	1 (CLA063, Li 2023); 1 (Individual 3, Sheppard 2023)	4 y (CLA063); male, congenital chylothorax at 3 weeks, 6 y at report (Sheppard 2023)	CCLA (Li 2023); congenital chylothorax + right leg lymphedema, no lymphatic imaging (Sheppard 2023)	sub-1% VAF requiring UMI error correction; extends KRAS→all CLA types framework; Sheppard 2023 Individual 3: mosaic KRAS G12V in nevus sebaceous with chylothorax and lymphedema (paper cites NM_004985.3)	Li 2023 Nat Med; Sheppard 2023 JCI Insight	PMC11184491; PMC10243805	37264205; 37154160	malformations/slow-flow/lm/complex/ccla
KRAS	G13D	c.38G>A	NM_004985.5	CCLA	10.3-38.8% (32.9% in NOF by exome)	nonossifying fibroma humerus + hyperpigmented skin + periosteum + muscle biopsies; blood and bone marrow NEGATIVE	whole-exome sequencing (clinical, GeneDX)	1	female child (chylous effusions age 9; DCMRL age 12)	central conducting (pulmonary lymphangiectasia, pleural effusions, peritoneal spillage, pelvic ascites)	oculoectodermal syndrome with aplasia cutis congenita and Blaschko-pattern hyperpigmentation; multi-tissue mosaicism with blood and bone marrow negative; failed ulixertinib (ERK inhibitor) for respiratory toxicity; on sirolimus	Sheppard 2023 JCI Insight	PMC10243805	37154160	malformations/slow-flow/lm/complex/ccla
KRAS	A146T	c.436G>A	NM_004985.5	CCLA	Li 2023: 3.9% (CLA163, single); Sheppard 2023: 3.3-3.4%	scrotal microcystic LM biopsy (keratinized squamous epithelium with D2-40+/CD31+ dilated lymphatics)	UPenn SOVM Panel v3 + research whole-exome sequencing (Sheppard); deep exome and/or UMI panel (Li 2023)	1 (17y male, Sheppard)	17y male (adolescent; symptoms from ~6-12y)	inguinal / scrotal / left lower extremity with retrograde flow to bilateral hemipelvis; central conducting involvement	mosaic in scrotal tissue; presented as lymphedema + chylous scrotal leak; topical sirolimus modestly effective (A146T itself was not functionally validated in Sheppard 2023)	Sheppard 2023 JCI Insight; Li 2023 Nat Med	PMC10243805; PMC11184491	37154160; 37264205	malformations/slow-flow/lm/complex/ccla
KRAS	Q61R	c.182A>G	NM_004985.5	GSD	1% (one sig fig per source)	affected lesion tissue (biopsy); lesion-restricted (undetectable in normal skin and blood)	amplicon-based deep sequencing, 50-gene cancer panel	1 (sole positive in a 6-patient GSD cohort)	n.r.	n.r.	Nozawa/Ozeki 2020 J Hum Genet (PMID 32591603); paywalled (no PMC); abstract-only read 2026-10-09	Nozawa/Ozeki 2020 J Hum Genet	n.r.	32591603	malformations/slow-flow/lm/complex/gsd
KRAS	Q70_Y71ins15	c.167_211dup	NM_004985.5	GLA	1.22%	gDNA tissue (CVA231)	UMI-based 49-gene panel (ultra-deep)	1 GLA	9 y (CVA231)	multifocal: mediastinal LM with bone, liver and splenic lesions (GLA; CVA231)	novel in-frame insertion (c.167_211dup, p.Gln70_Tyr71ins15); explicitly confirmed as novel KRAS variant	Li 2023 Nat Med	PMC11184491	37264205	malformations/slow-flow/lm/complex/gla
BRAF	V600E	c.1799T>A	NM_004333.6	LM	0.1-3.6% (ddPCR; Zenner Table 1)	lesion biopsy (LR17-322, LR19-346) + cell-free DNA from macrocystic cyst fluid (LR19-443)	VANseq 44-gene targeted panel + ddPCR + VE1 (BRAF V600E-specific) IHC	3	1 month, 5 months, 1 year (all infants, 0-5y)	cervicofacial (posterior lateral neck) x2; axilla x1; all de Serres stage 1 macrocystic	somatic mosaic; VE1 IHC-positive specifically in cyst-lining LECs (podoplanin+); paired skin (LR17-322, LR19-346), fat and muscle (LR19-346) NEGATIVE by ddPCR (tissue mosaicism; blood result not reported); cfDNA from aspirated cyst fluid diagnostic in LR19-443; 3% of 101-patient isolated-LM cohort	Zenner 2022 HGG Adv	PMC8972000	35373151	malformations/slow-flow/lm/isolated/lm
BRAF	V600E	c.1799T>A	NM_004333.6	GLA	0.2-8%	cfDNA from thoracic-duct lymphatic fluid + posterior mediastinal mass biopsy (Pt3); resected abdominal LM tissue (Pt4); cfDNA from pleural lymphatic fluid (Pt5); cfDNA from plasma + thoracic-duct fluid (Pt6)	UPenn SOVM Panel; CHOP Solid Tumor Panel; CHOP CAG research genetic panel	4 (Fox 2025); also GLA cases in Li 2023 (CVA119 at 0.21%, 21-month female)	CVA119 21 months female (Li); Pt3 age 3, Pt4 age 3, Pt5 age 16 months, Pt6 29-week preemie (Fox)	central conducting + mediastinum, spleen, mesentery, chest/abdomen/pelvis, hepatic; all with central conduction abnormality	Pt6 blood plasma-cfDNA-positive at 0.5% (rare non-tissue-restricted); treatment (Fox): Pt3 responded to diuretics + glue embolization and Pt4 to diuretics + low-fat high-protein diet, neither needing targeted pharmacotherapy; Pt5 responded to sirolimus + low-fat diet; Pt6 no treatment data (followed at outside institution); VAF as low as 0.21% detected via UMI-based error correction (Li 2023)	Fox 2025 Pediatr Blood Cancer; Li 2023 Nat Med	PMC12821086; PMC11184491	40884273; 37264205	malformations/slow-flow/lm/complex/gla
BRAF	V600E	c.1799T>A	NM_004333.6	KLA	0.2-2.2%	cell-free DNA from pleural lymphatic fluid; right pleura biopsy confirmed lymphatic (CD31+/D2-40+/PROX1+)	CHOP CAG research genetic panel (cfDNA sequencing)	1	adolescent (age 15 at chylothorax presentation; asymptomatic dx at 3y)	mediastinum, spleen, mesentery, chest/abdomen/pelvis, vertebral marrow, thoracic (with central conduction abnormality)	elevated Ang-2 (11,759 pg/mL); dual therapy dabrafenib+trametinib substantially improved outcome	Fox 2025 Pediatr Blood Cancer	PMC12821086	40884273	malformations/slow-flow/lm/complex/kla
BRAF	V600E	c.1799T>A	NM_004333.6	CCLA	Li 2023: 0.91% (CLA060); Fox 2025: 2.2-2.6% (Patient 1)	"gluteal skin biopsy (genetic testing ""from the biopsy""; colon resection used for pathology only) (Fox Pt1); tissue biopsy or fluid gDNA/cfDNA (Li 2023 cases)"	not specified for Pt1 (UPenn SOVM, CHOP Solid Tumor and CAG panels listed collectively in Methods) (Fox); deep exome + UMI-based 49-gene panel (Li 2023); BDA qPCR + Sanger validation	1 (Fox Pt1); additional cases in Li 2023	adolescent Pt1 (dx 13y; originally neonate mesenteric LM resected day 11) (Fox); pediatric cohort (Li 2023)	mesentery, gluteal skin, thoracic duct (central conducting) (Fox); CCLA (Li 2023)	Pt1 originally classified as isolated abdominal LM in neonate; central conduction abnormality manifested 13y post-resection with chylothorax; sequential sirolimus→trametinib→vemurafenib all discontinued for toxicity/lack of response (Fox); BRAF-F486S functionally validated by Li 2023 (increased p-ERK, sprouting; trametinib reversible)	Fox 2025 Pediatr Blood Cancer; Li 2023 Nat Med	PMC12821086; PMC11184491	40884273; 37264205	malformations/slow-flow/lm/complex/ccla
ARAF	S214P	c.640T>C	NM_001654.5	CCLA	n.r. (GoF)	blood (P1 and parents; P2 sample type n.r.)	WES (data in dbGaP phs001802.v1.p1)	2 (unrelated)	12 y (proband, M) + 1 unrelated adult	n.r.	Li D et al. Nat Med 2019;25:1116-1122 (PMID 31263281); main text paywalled (no PMC); abstract + open supplementary Methods read 2026-10-09 (blood specimens from P1 and parents; dbGaP phs001802.v1.p1)	Li D et al. Nat Med 2019 (ARAF; DOI 10.1038/s41591-019-0479-2)	n.r.	31263281	malformations/slow-flow/lm/complex/ccla
MAP2K1	F53C	c.158T>G	NM_002755.4	CCLA	gDNA (leftover cells): 0.66-0.83%; cfDNA (thoracic duct): 9.8-12.4%	cfDNA from thoracic duct fluid + gDNA from leftover cells after cfDNA spin-down	amplicon-based 35-gene panel + UMI-based 49-gene panel (dual confirmation)	1 (CLA135)	31 y (F; CLA135)	capillary malformation, right-sided lateralized overgrowth, chylous pericardial effusion, CCLA	novel LP variant (c.158T>G, p.F53C); MAP2K1 as candidate CCLA gene; higher VAF (~10-12%) in cfDNA fraction than in tissue gDNA (0.8%); dual sample confirmation	Li 2023 Nat Med	PMC11184491	37264205	malformations/slow-flow/lm/complex/ccla
CBL	Y774*	c.2322T>G	NM_005188.4	KLA	4% (WES, 20/493 reads); ~0.005% ddPCR (suboptimal input)	CD31-selected endothelial cells sorted from pleural chylous effusion fluid, expanded in culture; comparator negative samples: blood, saliva, skin fibroblasts, normal inguinal lymph node	Twist Human Core Exome Kit on Illumina NovaSeq 6000, 101-cycle paired-end, mean depth 338x; BWA/Mutect2 somatic calling; ANNOVAR/SnpEff annotation; Bio-Rad QX200 ddPCR validation	1	symptom onset 6y; KLA diagnosis after septic shock/effusions at 10y; rapamycin discontinuation and disease recrudescence at 18y; trametinib initiated at 18y	mediastinum, lungs, right breast/areola, axilla, spleen, sacrum, spine (bony involvement); pleural and pericardial chylous effusions	first report of CBL mutation in KLA; nonsense truncates negative regulator of RAS → GoF on RAS-MAPK; complete symptom resolution on trametinib; re-listed in Li 2023 as CLA054 (gDNA fluid, 4%, 19 y, deep exome + ddPCR validation)	Foster 2020 EMBO Mol Med; Li 2023 Nat Med	PMC7539180; PMC11184491	32894644; 37264205	malformations/slow-flow/lm/complex/kla
PIK3CA	P447_L455del	c.1338_1364del	NM_006218.3	LM	2.9%	lesional tissue (gDNA)	deep exome sequencing (~400-470x); validated by repeat UMI run	1 (CVA207)	6y female	common LM	novel in-frame 27-bp deletion (9 residues, P447_L455) in the PIK3CA C2 domain; single lesional sample; VAF 2.9%	Li 2023 Nat Med	PMC11184491	37264205	malformations/slow-flow/lm/isolated/lm
PIK3CA	*1069Pheext*4	c.3205_3206insTTTT	NM_006218.3	LM	n.r.	fresh/frozen affected tissue	custom 735-gene vascular-anomaly/cancer NGS panel (sensitive to ~1% mosaicism)	1 (novel LM-tissue variant; cohort 58 patients incl. 26 LM)	n.r.	n.r.	novel stop-loss variant: insertion at the PIK3CA termination codon reads through for 4 extra residues (p.*1069Pheext*4); one of two novel variants reported in LM tissue (with PIK3R1 E462_R465del); abstract-only (paywalled); functional effect not characterised	Henslee et al. 2026 Lymphatic Res Biol	n.r.	41574430	malformations/slow-flow/lm/isolated/lm
PIK3R1	E462_R465del	c.1384_1395del	NM_181523.3	LM	n.r.	lesional (affected) tissue biopsy	custom 735-gene vascular-anomaly/cancer NGS panel (sensitive to ~1% mosaicism)	1 (novel LM-tissue variant; cohort 58 patients incl. 26 LM)	n.r.	n.r.	novel PIK3R1 variant in LM tissue (one of two novel variants reported); PIK3R1 encodes the p85-alpha regulatory subunit of PI3K; abstract-only (paywalled)	Henslee et al. 2026 Lymphatic Res Biol	n.r.	41574430	malformations/slow-flow/lm/isolated/lm