Is CAPRIN1 p.Ser179= (c.537C>T) pathogenic?

CAPRIN1 p.Ser179= (c.537C>T) is classified Likely benign in CAPRIN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-05-14). Very rare (popmax 0.00333%, amr).

How common is CAPRIN1 p.Ser179= (c.537C>T) in the general population?

CAPRIN1 p.Ser179= (c.537C>T) is very rare (popmax 0.00333%, amr) (gnomAD).

CAPRIN1 p.Ser179=

c.537C>T · VCV4911206

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00333%, amr)

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 -3.9, phastCons 0.44
Overall
CADD	12.01	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00333% Admixed American · 2/59,994 alleles

Filtering AF 0.00223% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00198%

Overall 0.0026% 42/1,613,960 alleles · very rare exomes 38/1,461,866 · genomes 4/152,094 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00333%	29,997
Remaining individualsnot grpmax-eligible	0.0032%	31,242
European (non-Finnish)	0.00305%	32,779
African / African-American	0.00267%	37,435

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: CAPRIN1
Protein: p.Ser179=
Coding: c.537C>T
MANE Select: NM_005898
Type: single nucleotide variant
Location: chr11:34076406 (GRCh38)
Gene constraint: LOEUF 0.372 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 58.64 · 6 PDB

Full CAPRIN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CAPRIN1 p.Ser179Pro Uncertain significance ★ ⚠ same residue
CAPRIN1 p.Arg458Ter Pathogenic ★★ same type
CAPRIN1 p.Arg132Cys Uncertain significance ★★ ⚠ same type
CAPRIN1 p.Gln206Arg Uncertain significance ★★ ⚠ same type
CAPRIN1 p.Pro424Leu Uncertain significance ★★ ⚠ same type
CAPRIN1 p.Pro528Thr Uncertain significance ★★ ⚠ same type
CAPRIN1 c.1122+19G>A Benign ★★ same type
CAPRIN1 c.217-5C>G Likely pathogenic ★ 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/caprin1-p-ser179 (accessed [today's date]).

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