Is CABP4 p.Arg98Ter (c.292C>T) pathogenic?

CABP4 p.Arg98Ter (c.292C>T) is classified Pathogenic/Likely pathogenic in CABP4 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-02-07). Very rare (popmax 0.00348%, nfe); Associated with CABP4-related disorder.

What condition is associated with CABP4 p.Arg98Ter (c.292C>T)?

CABP4 p.Arg98Ter (c.292C>T) is associated with CABP4-related disorder, cone-rod synaptic disorder, congenital nonprogressive (ClinVar).

How common is CABP4 p.Arg98Ter (c.292C>T) in the general population?

CABP4 p.Arg98Ter (c.292C>T) is very rare (popmax 0.00348%, nfe) (gnomAD).

CABP4 p.Arg98Ter

c.292C>T · rs777555935 · VCV1184508

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00348%, nfe)

Conditions

CABP4-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 6
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.1	GERP 0.89, phastCons 1
Overall
CADD	38.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00348% European (non-Finnish) · 41/1,178,504 alleles

Filtering AF 0.00259% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00233%

Overall 0.00292% 47/1,608,258 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00348%	28,744
Remaining individualsnot grpmax-eligible	0.00321%	31,114
African / African-American	0.00267%	37,422
Admixed American	0.00168%	59,572
South Asian	0.00111%	90,248

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.Arg98Ter
Coding: c.292C>T
MANE Select: NM_145200
dbSNP: rs777555935
Type: single nucleotide variant
Location: chr11:67455715 (GRCh38)
Gene constraint: LOEUF 1.345 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.01
Residue 98: the 'disordered' region

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

Disease context

CABP4-related disorder

Also linked: cone-rod synaptic disorder, congenital nonprogressive

Similar variants

CABP4 p.Arg98Gln Uncertain significance ★ ⚠ same residue
CABP4 p.Arg98Gly Uncertain significance ★ ⚠ same residue
CABP4 c.366+1G>T Pathogenic/Likely pathogenic ★★ same condition
CABP4 p.Arg209Ter Pathogenic/Likely pathogenic ★★ same condition
CABP4 p.Arg216Ter Pathogenic ★★ same condition
CABP4 p.Arg225Ter Pathogenic ★★ same condition
CABP4 p.Arg49Ter Pathogenic/Likely pathogenic ★★ same condition
CABP4 p.Arg52Ter Pathogenic ★★ 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-arg98ter (accessed [today's date]).

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