Is CABP2 p.Asp159Val (c.476A>T) pathogenic?

CABP2 p.Asp159Val (c.476A>T) is classified Uncertain significance in CABP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-10). AlphaMissense: likely benign (0.3077); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CABP2 p.Asp159Val (c.476A>T)?

CABP2 p.Asp159Val (c.476A>T) is associated with Inborn genetic diseases (ClinVar).

How common is CABP2 p.Asp159Val (c.476A>T) in the general population?

CABP2 p.Asp159Val (c.476A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CABP2 p.Asp159Val (c.476A>T)?

AlphaMissense predicts likely benign (score 0.3077) — an in-silico prediction, not a clinical call.

CABP2 p.Asp159Val

c.476A>T · VCV3826533

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3077 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3077	likely benign
REVEL	0.577	indeterminate
SaProt	LLR -9.42	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.7	GERP -0.27, phastCons 0.73
Regional constraint	o/e 0.99	unconstrained · MANE · 4,184 bp · p 0.9 · regional, not allelic
Overall
CADD	24.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CABP2
Protein: p.Asp159Val
Coding: c.476A>T
MANE Select: NM_016366
Type: single nucleotide variant
Location: chr11:67520064 (GRCh38)
Gene constraint: LOEUF 1.299 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 68.93
Residue 159: a UniProt-annotated variant site (in dfnb93); the ef-hand 3 domain

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CABP2 p.Arg101Gln Uncertain significance ★★ ⚠ same condition
CABP2 p.Arg108Gln Uncertain significance ★★ ⚠ same condition
CABP2 p.Arg216Gln Uncertain significance ★★ ⚠ same condition
CABP2 p.Arg220Gln Uncertain significance ★★ ⚠ same condition
CABP2 p.Arg73Gln Uncertain significance ★★ ⚠ same condition
CABP2 p.Arg73Trp Uncertain significance ★★ ⚠ same condition
CABP2 p.Cys100Phe Uncertain significance ★★ ⚠ same condition
CABP2 p.Gly207Cys 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/cabp2-p-asp159val (accessed [today's date]).

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