Is CAPRIN2 p.Asn469Lys (c.1407C>G) pathogenic?

CAPRIN2 p.Asn469Lys (c.1407C>G) is classified Uncertain significance in CAPRIN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-03). Ultra-rare (popmax 0.0134%, afr).

How common is CAPRIN2 p.Asn469Lys (c.1407C>G) in the general population?

CAPRIN2 p.Asn469Lys (c.1407C>G) is ultra-rare (popmax 0.0134%, afr) (gnomAD).

CAPRIN2 p.Asn469Lys

c.1407C>G · VCV3827336

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.012	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.7	GERP -0.82, phastCons 0.82
Overall
CADD	13.09	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0134% African / African-American · 10/74,874 alleles

Filtering AF 0.00723% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0055%

Overall 0.00062% 10/1,613,930 alleles · ultra-rare

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: CAPRIN2
Protein: p.Asn469Lys
Coding: c.1407C>G
MANE Select: NM_001385503
Type: single nucleotide variant
Location: chr12:30728780 (GRCh38)
Gene constraint: LOEUF 0.58 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 52.42 · 5 PDB
Residue 469: the 'disordered' region

Full CAPRIN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CAPRIN2 c.1800+5C>T Benign ★★ same type
CAPRIN2 p.Met253Thr Benign ★★ same type
CAPRIN2 p.Ser668= Benign ★★ same type
CAPRIN2 p.Thr763= Benign ★★ same type
CAPRIN2 p.Tyr806= Benign ★★ same type
CAPRIN2 c.-12A>G Uncertain significance ★ same type
CAPRIN2 c.-2A>C Uncertain significance ★ same type
CAPRIN2 c.-30G>A 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/caprin2-p-asn469lys (accessed [today's date]).

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