Is CEP162 p.Cys4Phe (c.11G>T) pathogenic?

CEP162 p.Cys4Phe (c.11G>T) is classified Uncertain significance in CEP162 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-21). AlphaMissense: likely benign (0.0759); Absent from gnomAD v4.1.

How common is CEP162 p.Cys4Phe (c.11G>T) in the general population?

CEP162 p.Cys4Phe (c.11G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CEP162 p.Cys4Phe (c.11G>T)?

AlphaMissense predicts likely benign (score 0.0759) — an in-silico prediction, not a clinical call.

CEP162 p.Cys4Phe

c.11G>T · VCV3831720

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0759 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,569,144)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0759	likely benign
REVEL	0.046	moderately benign-leaning
SaProt	LLR -4.49	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.6	GERP -3.3
Regional constraint	o/e 1.01	unconstrained · MANE · 101 kb · p 0.75 · regional, not allelic
Overall
CADD	0.11	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,569,144). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CEP162
Protein: p.Cys4Phe
Coding: c.11G>T
MANE Select: NM_014895
Type: single nucleotide variant
Location: chr6:84226383 (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-cys4phe (accessed [today's date]).

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