Is RASA1 p.Gly485Arg (c.1453G>C) pathogenic?

RASA1 p.Gly485Arg (c.1453G>C) is classified Uncertain significance in RASA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-27). AlphaMissense: likely pathogenic (0.9545); Absent from gnomAD v4.1; Associated with capillary malformation-arteriovenous malformation syndrome.

What condition is associated with RASA1 p.Gly485Arg (c.1453G>C)?

RASA1 p.Gly485Arg (c.1453G>C) is associated with capillary malformation-arteriovenous malformation syndrome (ClinVar).

How common is RASA1 p.Gly485Arg (c.1453G>C) in the general population?

RASA1 p.Gly485Arg (c.1453G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about RASA1 p.Gly485Arg (c.1453G>C)?

AlphaMissense predicts likely pathogenic (score 0.9545) — an in-silico prediction, not a clinical call.

RASA1 p.Gly485Arg

c.1453G>C · VCV4714022

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9545 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

capillary malformation-arteriovenous malformation syndrome

Computational evidence

Protein change
AlphaMissense	0.9545	likely pathogenic
REVEL	0.189	benign-leaning
SaProt	LLR -9.18	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5.2	GERP 0.037, phastCons 1
Regional constraint	o/e 0.67	unconstrained · MANE · 18 kb · p 2.3e-14 · regional, not allelic
Overall
CADD	26.2	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: RASA1
Protein: p.Gly485Arg
Coding: c.1453G>C
MANE Select: NM_001239 · reported on NM_002890
Type: single nucleotide variant
Location: chr5:87362671 (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-gly485arg (accessed [today's date]).

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