Is RASA1 p.Pro120= (c.360C>A) pathogenic?

RASA1 p.Pro120= (c.360C>A) is classified Benign/Likely benign in RASA1 (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-01-19). Rare (popmax 0.132%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with RASA1 p.Pro120= (c.360C>A)?

RASA1 p.Pro120= (c.360C>A) is associated with Cardiovascular phenotype, basal cell carcinoma, susceptibility to, 1, capillary malformation-arteriovenous malformation syndrome (ClinVar).

How common is RASA1 p.Pro120= (c.360C>A) in the general population?

RASA1 p.Pro120= (c.360C>A) is rare (popmax 0.132%, nfe) (gnomAD).

RASA1 p.Pro120=

c.360C>A · rs137878395 · VCV354509

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Rare

rare (popmax 0.132%, nfe)

Conditions

Cardiovascular phenotype

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 0.59	GERP 0.32, phastCons 0.52
Overall
CADD	10.98	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.132% European (non-Finnish) · 1,561/1,180,030 alleles

Filtering AF 0.127% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.125%

Overall 0.102% 1,650/1,613,968 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.132%	756
Remaining individualsnot grpmax-eligible	0.0928%	1,077
Middle Eastern	0.0493%	2,028
Admixed American	0.0233%	4,285
African / African-American	0.016%	6,243
Finnishnot grpmax-eligible	0.00313%	31,985

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.Pro120=
Coding: c.360C>A
MANE Select: NM_002890
dbSNP: rs137878395
Type: single nucleotide variant
Location: chr5:87268811 (GRCh38)
Gene constraint: LOEUF 0.3 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.37 · 15 PDB

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: basal cell carcinoma, susceptibility to, 1 capillary malformation-arteriovenous malformation syndrome capillary malformation-arteriovenous malformation 1

Similar variants

RASA1 p.Pro120Arg Uncertain significance ★ ⚠ same residue
RASA1 p.Pro120Ser Uncertain significance ★ ⚠ same residue
RASA1 p.Ala115Gly Uncertain significance ★★ ⚠ same condition
RASA1 p.Ala115Val Uncertain significance ★★ ⚠ same condition
RASA1 p.Ala125Gly Uncertain significance ★★ ⚠ same condition
RASA1 p.Ala23Thr Uncertain significance ★★ ⚠ same condition
RASA1 p.Ala29Val Uncertain significance ★★ ⚠ same condition
RASA1 p.Ala32Val Uncertain significance ★★ ⚠ same condition

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-pro120 (accessed [today's date]).

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