Is CABP4 p.Arg124= (c.372C>T) pathogenic?

CABP4 p.Arg124= (c.372C>T) is classified Likely benign in CABP4 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-05-10). Ultra-rare (popmax 0.0134%, eas); Associated with Inborn genetic diseases.

What condition is associated with CABP4 p.Arg124= (c.372C>T)?

CABP4 p.Arg124= (c.372C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CABP4 p.Arg124= (c.372C>T) in the general population?

CABP4 p.Arg124= (c.372C>T) is ultra-rare (popmax 0.0134%, eas) (gnomAD).

CABP4 p.Arg124=

c.372C>T · rs199875527 · VCV1147934

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, eas)

Conditions

Inborn genetic diseases

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 -8.9	GERP -4.6
Overall
CADD	0.159	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0134% East Asian · 6/44,836 alleles

Filtering AF 0.00579% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00394%

Overall 0.0026% 42/1,613,192 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0134%	7,473
Finnishnot grpmax-eligible	0.0126%	7,915
Admixed American	0.00333%	30,009
European (non-Finnish)	0.00203%	49,163
Remaining individualsnot grpmax-eligible	0.0016%	62,496
South Asian	0.0011%	91,078

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: CABP4
Protein: p.Arg124=
Coding: c.372C>T
MANE Select: NM_145200
dbSNP: rs199875527
Type: single nucleotide variant
Location: chr11:67456193 (GRCh38)
Gene constraint: LOEUF 1.345 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.01
Residue 124: a UniProt-annotated variant site (in crsd)

Full CABP4 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

CABP4 p.Arg124Leu Uncertain significance ★ ⚠ same residue
CABP4 p.Arg124Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
CABP4 p.Arg124His Conflicting classifications of pathogenicity ★ same residue
CABP4 p.Arg124fs Pathogenic/Likely pathogenic ★★ same residue
CABP4 p.Ala107Thr Uncertain significance ★★ ⚠ same condition
CABP4 p.Ala108Thr Uncertain significance ★★ ⚠ same condition
CABP4 p.Ala137Thr Uncertain significance ★★ same condition
CABP4 p.Ala203Val 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/cabp4-p-arg124 (accessed [today's date]).

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