Is CEP162 p.His1168Pro (c.3503A>C) pathogenic?

CEP162 p.His1168Pro (c.3503A>C) is classified Uncertain significance in CEP162 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-14). AlphaMissense: likely benign (0.1432); Absent from gnomAD v4.1.

How common is CEP162 p.His1168Pro (c.3503A>C) in the general population?

CEP162 p.His1168Pro (c.3503A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CEP162 p.His1168Pro (c.3503A>C)?

AlphaMissense predicts likely benign (score 0.1432) — an in-silico prediction, not a clinical call.

CEP162 p.His1168Pro

c.3503A>C · VCV4000681

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1432 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1432	likely benign
REVEL	0.165	moderately benign-leaning
SaProt	LLR -7.07	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 -0.064	GERP -4.2, phastCons 0.002
Regional constraint	o/e 1.01	unconstrained · MANE · 101 kb · p 0.75 · regional, not allelic
Overall
CADD	16.41	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CEP162
Protein: p.His1168Pro
Coding: c.3503A>C
MANE Select: NM_014895
Type: single nucleotide variant
Location: chr6:84152671 (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-his1168pro (accessed [today's date]).

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