Is CEP164 p.Ala132Ser (c.394G>T) pathogenic?

CEP164 p.Ala132Ser (c.394G>T) is classified Uncertain significance in CEP164 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-12). AlphaMissense: likely benign (0.0934); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CEP164 p.Ala132Ser (c.394G>T)?

CEP164 p.Ala132Ser (c.394G>T) is associated with Inborn genetic diseases (ClinVar).

How common is CEP164 p.Ala132Ser (c.394G>T) in the general population?

CEP164 p.Ala132Ser (c.394G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CEP164 p.Ala132Ser (c.394G>T)?

AlphaMissense predicts likely benign (score 0.0934) — an in-silico prediction, not a clinical call.

CEP164 p.Ala132Ser

c.394G>T · rs1288421627 · VCV2317872

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0934 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0934	likely benign
REVEL	0.089	moderately benign-leaning
SaProt	LLR -5.30	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 9.9	GERP 1.4, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 74 kb · p 0.19 · regional, not allelic
Overall
CADD	25.0	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: CEP164
Protein: p.Ala132Ser
Coding: c.394G>T
MANE Select: NM_014956
dbSNP: rs1288421627
Type: single nucleotide variant
Location: chr11:117361835 (GRCh38)
Gene constraint: LOEUF 1.009 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.08 · 4 PDB
Residue 132: the 'interaction with atrip' region; the 'disordered' region

Full CEP164 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

CEP164 p.Ala132Gly Benign ★★ same residue
CEP164 p.Ala132= Likely benign ★ same residue
CEP164 c.3089+6G>A Uncertain significance ★★ same condition
CEP164 p.Ala1105Val Uncertain significance ★★ ⚠ same condition
CEP164 p.Ala1145Val Uncertain significance ★★ ⚠ same condition
CEP164 p.Ala952Thr Uncertain significance ★★ ⚠ same condition
CEP164 p.Arg1122Pro Uncertain significance ★★ ⚠ same condition
CEP164 p.Arg1125Trp 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/cep164-p-ala132ser (accessed [today's date]).

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