Is CEP152 p.Arg264Cys (c.790C>T) pathogenic?

CEP152 p.Arg264Cys (c.790C>T) is classified Conflicting classifications of pathogenicity in CEP152 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2023-12-13). AlphaMissense: likely benign (0.1236); Ultra-rare (popmax 0.0213%, afr); Associated with Inborn genetic diseases.

What condition is associated with CEP152 p.Arg264Cys (c.790C>T)?

CEP152 p.Arg264Cys (c.790C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CEP152 p.Arg264Cys (c.790C>T) in the general population?

CEP152 p.Arg264Cys (c.790C>T) is ultra-rare (popmax 0.0213%, afr) (gnomAD).

What do computational predictors say about CEP152 p.Arg264Cys (c.790C>T)?

AlphaMissense predicts likely benign (score 0.1236) — an in-silico prediction, not a clinical call.

CEP152 p.Arg264Cys

c.790C>T · rs146482586 · VCV1392072

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1236 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0213%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1236	likely benign
REVEL	0.335	indeterminate
SaProt	LLR -7.63	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 5.9	GERP 3.7, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 67 kb · p 0.21 · regional, not allelic
Overall
CADD	24.2	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0213% African / African-American · 16/75,010 alleles

Filtering AF 0.0133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0109%

Overall 0.00229% 37/1,613,874 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0213%	4,688
Remaining individualsnot grpmax-eligible	0.0144%	6,945
Admixed American	0.00167%	60,006
South Asian	0.0011%	91,074
European (non-Finnish)	0.000848%	117,992

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: CEP152
Protein: p.Arg264Cys
Coding: c.790C>T
MANE Select: NM_001194998
dbSNP: rs146482586
Type: single nucleotide variant
Location: chr15:48793363 (GRCh38)
Gene constraint: LOEUF 0.784 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.54 · 3 PDB

Full CEP152 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

CEP152 p.Arg264His Uncertain significance ★★ ⚠ same residue
CEP152 p.Arg264Leu Uncertain significance ★ ⚠ same residue
CEP152 c.540+6G>A Uncertain significance ★★ same condition
CEP152 p.Ala165Gly Uncertain significance ★★ ⚠ same condition
CEP152 p.Ala411Thr Uncertain significance ★★ ⚠ same condition
CEP152 p.Ala956Val Uncertain significance ★★ ⚠ same condition
CEP152 p.Arg1034Gln Uncertain significance ★★ ⚠ same condition
CEP152 p.Arg1283Cys 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/cep152-p-arg264cys (accessed [today's date]).

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