Is RASA1 p.Arg913= (c.2739G>C) pathogenic?

RASA1 p.Arg913= (c.2739G>C) is classified Likely benign in RASA1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-04-13). Ultra-rare (popmax 0.0217%, amr); Associated with Cardiovascular phenotype.

What condition is associated with RASA1 p.Arg913= (c.2739G>C)?

RASA1 p.Arg913= (c.2739G>C) is associated with Cardiovascular phenotype, capillary malformation-arteriovenous malformation syndrome (ClinVar).

How common is RASA1 p.Arg913= (c.2739G>C) in the general population?

RASA1 p.Arg913= (c.2739G>C) is ultra-rare (popmax 0.0217%, amr) (gnomAD).

RASA1 p.Arg913=

c.2739G>C · rs375135791 · VCV1566891

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0217%, amr)

Conditions

Cardiovascular phenotype

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

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 7.6	GERP 2.8, phastCons 1
Overall
CADD	12.49	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0217% Admixed American · 13/59,778 alleles

Filtering AF 0.0128% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0102%

Overall 0.00199% 32/1,610,966 alleles · ultra-rare exomes 26/1,459,846 · genomes 6/151,120 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0217%	4,598
Remaining individualsnot grpmax-eligible	0.0016%	62,364
European (non-Finnish)	0.00153%	65,487

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.Arg913=
Coding: c.2739G>C
MANE Select: NM_002890
dbSNP: rs375135791
Type: single nucleotide variant
Location: chr5:87383761 (GRCh38)

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: capillary malformation-arteriovenous malformation syndrome

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-arg913 (accessed [today's date]).

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