Is CABP4 p.Asp144Val (c.431A>T) pathogenic?

CABP4 p.Asp144Val (c.431A>T) is classified Uncertain significance in CABP4 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-11-08). AlphaMissense: likely pathogenic (0.838); Absent from gnomAD v4.1.

How common is CABP4 p.Asp144Val (c.431A>T) in the general population?

CABP4 p.Asp144Val (c.431A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CABP4 p.Asp144Val (c.431A>T)?

AlphaMissense predicts likely pathogenic (score 0.838) — an in-silico prediction, not a clinical call.

CABP4 p.Asp144Val

c.431A>T · rs1864792998 · VCV972208

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.838 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.838	likely pathogenic
REVEL	0.851	moderately pathogenic-leaning
SaProt	LLR -12.83	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.5, phastCons 1
Regional constraint	o/e 1.07	unconstrained · MANE · 3,232 bp · p 0.15 · regional, not allelic
Overall
CADD	28.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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: CABP4
Protein: p.Asp144Val
Coding: c.431A>T
MANE Select: NM_145200
dbSNP: rs1864792998
Type: single nucleotide variant
Location: chr11:67456332 (GRCh38)
Gene constraint: LOEUF 1.345 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.01
Residue 144: the ef-hand 1 domain; a binding site

Full CABP4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CABP4 p.Asp144= Uncertain significance ★ same residue
CABP4 c.366+1G>T Pathogenic/Likely pathogenic ★★ same type
CABP4 p.Arg209Ter Pathogenic/Likely pathogenic ★★ same type
CABP4 p.Arg216Ter Pathogenic ★★ same type
CABP4 p.Arg225Ter Pathogenic ★★ same type
CABP4 p.Arg49Ter Pathogenic/Likely pathogenic ★★ same type
CABP4 p.Arg52Ter Pathogenic ★★ same type
CABP4 p.Arg98Ter Pathogenic/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/cabp4-p-asp144val (accessed [today's date]).

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