Is CEP70 p.Ala5Pro (c.13G>C) pathogenic?

CEP70 p.Ala5Pro (c.13G>C) is classified Uncertain significance in CEP70 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-06). AlphaMissense: likely benign (0.0948); Absent from gnomAD v4.1.

How common is CEP70 p.Ala5Pro (c.13G>C) in the general population?

CEP70 p.Ala5Pro (c.13G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CEP70 p.Ala5Pro (c.13G>C)?

AlphaMissense predicts likely benign (score 0.0948) — an in-silico prediction, not a clinical call.

CEP70 p.Ala5Pro

c.13G>C · VCV4001132

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0948 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0948	likely benign
REVEL	0.118	moderately benign-leaning
SaProt	LLR -5.76	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.47	acceptor gain · deltas
Pangolin	Δ0.23	gain · loss 0.10 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 0.11	GERP 2.5, phastCons 0.11
Regional constraint	o/e 0.97	unconstrained · MANE · 78 kb · p 0.42 · regional, not allelic
Overall
CADD	19.09	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: CEP70
Protein: p.Ala5Pro
Coding: c.13G>C
MANE Select: NM_024491
Type: single nucleotide variant
Location: chr3:138572915 (GRCh38)
Gene constraint: LOEUF 1.077 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.91
Residue 5: the 'disordered' region

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.Arg165Gln Uncertain significance ★ ⚠ same type
CEP70 p.Arg165Gly Uncertain significance ★ ⚠ same type
CEP70 p.Arg165Ter Uncertain significance ★ same type
CEP70 p.Arg189His 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-ala5pro (accessed [today's date]).

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