Is RASA2 p.Pro293= (c.879A>G) pathogenic?

RASA2 p.Pro293= (c.879A>G) is classified Likely benign in RASA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-12). Very rare (popmax 0.00224%, eas).

How common is RASA2 p.Pro293= (c.879A>G) in the general population?

RASA2 p.Pro293= (c.879A>G) is very rare (popmax 0.00224%, eas) (gnomAD).

RASA2 p.Pro293=

c.879A>G · rs1278484386 · VCV1764675

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00224%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.27	GERP -3.7, phastCons 0.36
Overall
CADD	5.991	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00224% East Asian · 1/44,546 alleles

Overall 0.000124% 2/1,608,232 alleles · very rare exomes 2/1,455,942 · genomes 0/152,290 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00224%	44,546
African / African-American	0.00134%	74,598

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: RASA2
Protein: p.Pro293=
Coding: c.879A>G
MANE Select: NM_006506
dbSNP: rs1278484386
Type: single nucleotide variant
Location: chr3:141570927 (GRCh38)
Gene constraint: LOEUF 1.484 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.63

Full RASA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RASA2 p.Pro293Ser Uncertain significance ★ same residue
RASA2 c.612-3C>T Uncertain significance ★★ same type
RASA2 p.Ala360Gly Uncertain significance ★★ same type
RASA2 p.Ala489Thr Uncertain significance ★★ same type
RASA2 p.Ala503Ser Uncertain significance ★★ same type
RASA2 p.Ala742Val Uncertain significance ★★ same type
RASA2 p.Arg117His Uncertain significance ★★ same type
RASA2 p.Arg310Gln Uncertain significance ★★ same type

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/rasa2-p-pro293 (accessed [today's date]).

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