Is RASA1 p.Ser509= (c.1527C>T) pathogenic?

RASA1 p.Ser509= (c.1527C>T) is classified Likely benign in RASA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-31). Very rare (popmax 0.00671%, eas); Associated with capillary malformation-arteriovenous malformation syndrome.

What condition is associated with RASA1 p.Ser509= (c.1527C>T)?

RASA1 p.Ser509= (c.1527C>T) is associated with capillary malformation-arteriovenous malformation syndrome (ClinVar).

How common is RASA1 p.Ser509= (c.1527C>T) in the general population?

RASA1 p.Ser509= (c.1527C>T) is very rare (popmax 0.00671%, eas) (gnomAD).

RASA1 p.Ser509=

c.1527C>T · rs777268855 · VCV2185527

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00671%, eas)

Conditions

capillary malformation-arteriovenous malformation syndrome

⚠ 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 2.9	GERP 0.1, phastCons 1
Overall
CADD	12.47	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00671% East Asian · 3/44,720 alleles

Filtering AF 0.00178% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000893%

Overall 0.000373% 6/1,610,396 alleles · very rare exomes 5/1,458,856 · genomes 1/151,540 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00671%	14,907
European (non-Finnish)	0.000255%	392,460

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.Ser509=
Coding: c.1527C>T
MANE Select: NM_002890
dbSNP: rs777268855
Type: single nucleotide variant
Location: chr5:87363421 (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-ser509 (accessed [today's date]).

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