Is RASA1 p.Lys303= (c.909A>G) pathogenic?

RASA1 p.Lys303= (c.909A>G) is classified Likely benign in RASA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-09). Ultra-rare (popmax 0.0166%, mid); Associated with capillary malformation-arteriovenous malformation syndrome.

What condition is associated with RASA1 p.Lys303= (c.909A>G)?

RASA1 p.Lys303= (c.909A>G) is associated with capillary malformation-arteriovenous malformation syndrome (ClinVar).

How common is RASA1 p.Lys303= (c.909A>G) in the general population?

RASA1 p.Lys303= (c.909A>G) is ultra-rare (popmax 0.0166%, mid) (gnomAD).

RASA1 p.Lys303=

c.909A>G · rs765093179 · VCV1365972

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0166%, mid)

Conditions

capillary malformation-arteriovenous malformation syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 3.6	GERP 0.42, phastCons 1
Overall
CADD	8.62	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0166% Middle Eastern · 1/6,028 alleles

Filtering AF 0.00107% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000496%

Overall 0.000498% 8/1,605,946 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0166%	6,028
African / African-American	0.00402%	24,867
Remaining individualsnot grpmax-eligible	0.00322%	31,051
South Asian	0.00226%	44,322

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: RASA1
Protein: p.Lys303=
Coding: c.909A>G
MANE Select: NM_001239 · reported on NM_002890
dbSNP: rs765093179
Type: single nucleotide variant
Location: chr5:87337983 (GRCh38)

Full RASA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

capillary malformation-arteriovenous malformation syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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/rasa1-p-lys303 (accessed [today's date]).

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