Is CEP70 p.Pro362Ala (c.1084C>G) pathogenic?

CEP70 p.Pro362Ala (c.1084C>G) is classified Likely benign in CEP70 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-01). AlphaMissense: likely benign (0.1505); Rare (popmax 0.163%, amr).

How common is CEP70 p.Pro362Ala (c.1084C>G) in the general population?

CEP70 p.Pro362Ala (c.1084C>G) is rare (popmax 0.163%, amr) (gnomAD).

What do computational predictors say about CEP70 p.Pro362Ala (c.1084C>G)?

AlphaMissense predicts likely benign (score 0.1505) — an in-silico prediction, not a clinical call.

CEP70 p.Pro362Ala

c.1084C>G · rs61996332 · VCV2654192

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1505 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.163%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1505	likely benign
REVEL	0.255	benign-leaning
SaProt	LLR -7.28	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 8.2	GERP 1.2, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 78 kb · p 0.42 · regional, not allelic
Overall
CADD	24.9	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 0.163% Admixed American · 96/59,040 alleles

Filtering AF 0.137% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.134%

Overall 0.119% 1,915/1,606,790 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.163%	615
European (non-Finnish)	0.142%	702
Remaining individualsnot grpmax-eligible	0.141%	707
Ashkenazi Jewishnot grpmax-eligible	0.0885%	1,129
Finnishnot grpmax-eligible	0.0191%	5,242
African / African-American	0.0174%	5,738
Middle Eastern	0.0166%	6,016
South Asian	0.00223%	44,854

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: CEP70
Protein: p.Pro362Ala
Coding: c.1084C>G
MANE Select: NM_024491
dbSNP: rs61996332
Type: single nucleotide variant
Location: chr3:138505432 (GRCh38)
Gene constraint: LOEUF 1.077 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.91

Full CEP70 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP70 c.1732+103G>C Uncertain significance ★ same type
CEP70 p.Ala198Val Uncertain significance ★ ⚠ same type
CEP70 p.Ala251Thr Uncertain significance ★ ⚠ same type
CEP70 p.Ala588Ser Uncertain significance ★ ⚠ same type
CEP70 p.Ala5Pro Uncertain significance ★ ⚠ same type
CEP70 p.Arg165Gln Uncertain significance ★ ⚠ same type
CEP70 p.Arg165Gly Uncertain significance ★ ⚠ same type
CEP70 p.Arg165Ter 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/cep70-p-pro362ala (accessed [today's date]).

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