Is RASA1 p.Cys261= (c.783T>C) pathogenic?

RASA1 p.Cys261= (c.783T>C) is classified Likely benign in RASA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-20). Very rare (popmax 0.00224%, eas); Associated with capillary malformation-arteriovenous malformation syndrome.

What condition is associated with RASA1 p.Cys261= (c.783T>C)?

RASA1 p.Cys261= (c.783T>C) is associated with capillary malformation-arteriovenous malformation syndrome (ClinVar).

How common is RASA1 p.Cys261= (c.783T>C) in the general population?

RASA1 p.Cys261= (c.783T>C) is very rare (popmax 0.00224%, eas) (gnomAD).

RASA1 p.Cys261=

c.783T>C · VCV4733367

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00224%, eas)

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 6.1	GERP 2.8, phastCons 1
Overall
CADD	13.61	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00224% East Asian · 1/44,692 alleles

Overall 0.000658% 1/152,042 alleles · very rare

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.Cys261=
Coding: c.783T>C
MANE Select: NM_001239 · reported on NM_002890
Type: single nucleotide variant
Location: chr5:87332597 (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-cys261 (accessed [today's date]).

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