Is CABP2 p.Arg10Ser (c.28C>A) pathogenic?

CABP2 p.Arg10Ser (c.28C>A) is classified Likely benign in CABP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-08-28). AlphaMissense: likely benign (0.1566); Very rare (popmax 0.000435%, nfe).

How common is CABP2 p.Arg10Ser (c.28C>A) in the general population?

CABP2 p.Arg10Ser (c.28C>A) is very rare (popmax 0.000435%, nfe) (gnomAD).

What do computational predictors say about CABP2 p.Arg10Ser (c.28C>A)?

AlphaMissense predicts likely benign (score 0.1566) — an in-silico prediction, not a clinical call.

CABP2 p.Arg10Ser

c.28C>A · VCV4912605

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1566 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000435%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1566	likely benign
REVEL	0.143	moderately benign-leaning
SaProt	LLR -6.04	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.9	GERP 0.43, phastCons 0.009
Regional constraint	o/e 0.99	unconstrained · MANE · 4,184 bp · p 0.9 · regional, not allelic
Overall
CADD	15.92	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000435% European (non-Finnish) · 5/1,149,148 alleles

Filtering AF 0.000128% ClinGen BA1/BS1 input FAF95, joint · FAF99 9.3e-05%

Overall 0.000356% 5/1,403,222 alleles · very 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: CABP2
Protein: p.Arg10Ser
Coding: c.28C>A
MANE Select: NM_016366
Type: single nucleotide variant
Location: chr11:67523299 (GRCh38)
Gene constraint: LOEUF 1.299 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 68.93
Residue 10: the 'disordered' region

Full CABP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CABP2 p.Arg10His Conflicting classifications of pathogenicity ★ ⚠ same residue
CABP2 c.637+1G>T Pathogenic/Likely pathogenic ★★ same type
CABP2 p.Ala183Thr Uncertain significance ★★ ⚠ same type
CABP2 p.Arg101Gln Uncertain significance ★★ ⚠ same type
CABP2 p.Arg108Gln Uncertain significance ★★ ⚠ same type
CABP2 p.Arg11Gln Uncertain significance ★★ ⚠ same type
CABP2 p.Arg216Gln Uncertain significance ★★ ⚠ same type
CABP2 p.Arg220Gln 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/cabp2-p-arg10ser (accessed [today's date]).

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