Is FLT4 p.Pro1008Leu (c.3023C>T) pathogenic?

FLT4 p.Pro1008Leu (c.3023C>T) is classified Conflicting classifications of pathogenicity in FLT4 (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2023-10-14). AlphaMissense: likely benign (0.1709); Rare (popmax 0.129%, nfe); Associated with lymphatic malformation 1.

What condition is associated with FLT4 p.Pro1008Leu (c.3023C>T)?

FLT4 p.Pro1008Leu (c.3023C>T) is associated with lymphatic malformation 1 (ClinVar).

How common is FLT4 p.Pro1008Leu (c.3023C>T) in the general population?

FLT4 p.Pro1008Leu (c.3023C>T) is rare (popmax 0.129%, nfe) (gnomAD).

How is Milroy disease inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about FLT4 p.Pro1008Leu (c.3023C>T)?

AlphaMissense predicts likely benign (score 0.1709) — an in-silico prediction, not a clinical call.

FLT4 p.Pro1008Leu

c.3023C>T · rs149033942 · VCV1297745

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.1709 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.129%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

lymphatic malformation 1

Computational evidence

Protein change
AlphaMissense	0.1709	likely benign
REVEL	0.651	pathogenic-leaning
SaProt	LLR -10.14	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP -3.9, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 15 kb · p 1.4e-05 · regional, not allelic
Overall
CADD	26.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.129% European (non-Finnish) · 1,521/1,179,910 alleles

Filtering AF 0.123% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.121%

Overall 0.0979% 1,579/1,613,096 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.129%	776
Remaining individualsnot grpmax-eligible	0.048%	2,082
African / African-American	0.0227%	4,405
Admixed American	0.0133%	7,498
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,604
East Asian	0.00223%	44,894
Finnishnot grpmax-eligible	0.00158%	63,266

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: FLT4
Protein: p.Pro1008Leu
Coding: c.3023C>T
MANE Select: NM_182925
dbSNP: rs149033942
Type: single nucleotide variant
Location: chr5:180616973 (GRCh38)
Gene constraint: LOEUF 0.265 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 72.82 · 2 PDB
Residue 1008: the protein kinase domain; a UniProt-annotated variant site (in chtd7)

Full FLT4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

lymphatic malformation 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Milroy disease (Orphanet):

Inheritance: Autosomal dominant
Onset: Antenatal, Infancy, Neonatal

Similar variants

FLT4 p.Arg1041Gln Pathogenic/Likely pathogenic ★★ same condition
FLT4 p.Arg1041Trp Pathogenic/Likely pathogenic ★★ same condition
FLT4 p.Gly857Arg Pathogenic ★★ same condition
FLT4 p.Pro1137Leu Likely pathogenic ★★ same condition
FLT4 p.Ala702Ser Uncertain significance ★★ ⚠ same condition
FLT4 p.Ala855Thr Uncertain significance ★★ ⚠ same condition
FLT4 p.Arg1060Gln Uncertain significance ★★ ⚠ same condition
FLT4 p.Arg1070Cys Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/flt4-p-pro1008leu (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown