Is CEP162 p.Phe13Cys (c.38T>G) pathogenic?

CEP162 p.Phe13Cys (c.38T>G) is classified Uncertain significance in CEP162 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-30). AlphaMissense: likely pathogenic (0.9026); Ultra-rare (popmax 0.0255%, eas).

How common is CEP162 p.Phe13Cys (c.38T>G) in the general population?

CEP162 p.Phe13Cys (c.38T>G) is ultra-rare (popmax 0.0255%, eas) (gnomAD).

What do computational predictors say about CEP162 p.Phe13Cys (c.38T>G)?

AlphaMissense predicts likely pathogenic (score 0.9026) — an in-silico prediction, not a clinical call.

CEP162 p.Phe13Cys

c.38T>G · rs749447084 · VCV3142611

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9026 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0255%, eas)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9026	likely pathogenic · top 3% in CEP162
REVEL	0.229	benign-leaning
SaProt	LLR -12.43	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.6, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 101 kb · p 0.75 · regional, not allelic
Overall
CADD	27.6	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 0.0255% East Asian · 11/43,174 alleles

Filtering AF 0.0142% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.011%

Overall 0.000703% 11/1,564,556 alleles · ultra-rare

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: CEP162
Protein: p.Phe13Cys
Coding: c.38T>G
MANE Select: NM_014895
dbSNP: rs749447084
Type: single nucleotide variant
Location: chr6:84226356 (GRCh38)
Gene constraint: LOEUF 1.101 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.93

Full CEP162 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP162 p.Leu1052Pro Uncertain significance ★★ ⚠ same type
CEP162 c.687+3A>G Uncertain significance ★ same type
CEP162 p.Ala1224Val Uncertain significance ★ ⚠ same type
CEP162 p.Ala1359Gly Uncertain significance ★ ⚠ same type
CEP162 p.Ala190Thr Uncertain significance ★ ⚠ same type
CEP162 p.Ala375Asp Uncertain significance ★ ⚠ same type
CEP162 p.Ala494Thr Uncertain significance ★ ⚠ same type
CEP162 p.Ala508Val Uncertain significance ★ ⚠ 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/cep162-p-phe13cys (accessed [today's date]).

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