Is CABP4 p.Phe120= (c.360C>T) pathogenic?

CABP4 p.Phe120= (c.360C>T) is classified Benign/Likely benign in CABP4 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-01-26). Rare (popmax 0.639%, nfe); Associated with cone-rod synaptic disorder, congenital nonprogressive.

What condition is associated with CABP4 p.Phe120= (c.360C>T)?

CABP4 p.Phe120= (c.360C>T) is associated with cone-rod synaptic disorder, congenital nonprogressive (ClinVar).

How common is CABP4 p.Phe120= (c.360C>T) in the general population?

CABP4 p.Phe120= (c.360C>T) is rare (popmax 0.639%, nfe) (gnomAD).

CABP4 p.Phe120=

c.360C>T · rs192900242 · VCV305647

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.639%, nfe)

Conditions

cone-rod synaptic disorder, congenital nonprogressive

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 -9.5	GERP -4.3
Overall
CADD	6.631	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.639% European (non-Finnish) · 7,411/1,159,522 alleles

Filtering AF 0.627% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.622%

Overall 0.517% 8,131/1,572,306 alleles · rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	3.84%	26
European (non-Finnish)grpmax	0.639%	156
Remaining individualsnot grpmax-eligible	0.469%	213
Admixed American	0.363%	275
Middle Eastern	0.283%	354
Ashkenazi Jewishnot grpmax-eligible	0.16%	626
African / African-American	0.111%	905
Finnishnot grpmax-eligible	0.055%	1,817
South Asian	0.0303%	3,303
East Asian	0.00234%	42,668

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Phe120=
Coding: c.360C>T
MANE Select: NM_145200
dbSNP: rs192900242
Type: single nucleotide variant
Location: chr11:67455783 (GRCh38)
Gene constraint: LOEUF 1.345 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.01

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

Disease context

cone-rod synaptic disorder, congenital nonprogressive — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

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
CABP4 p.Arg98Ter Pathogenic/Likely pathogenic ★★ same condition
CABP4 c.*1117C>A Uncertain significance ★★ same condition
CABP4 c.*1158A>G 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-phe120 (accessed [today's date]).

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