Is COQ7 p.Ser22Pro (c.64T>C) pathogenic?

COQ7 p.Ser22Pro (c.64T>C) is classified Likely benign in COQ7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-11). AlphaMissense: likely benign (0.0592); Absent from gnomAD v4.1.

How common is COQ7 p.Ser22Pro (c.64T>C) in the general population?

COQ7 p.Ser22Pro (c.64T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about COQ7 p.Ser22Pro (c.64T>C)?

AlphaMissense predicts likely benign (score 0.0592) — an in-silico prediction, not a clinical call.

COQ7 p.Ser22Pro

c.64T>C · VCV4005844

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0592 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0592	likely benign
REVEL	0.046	moderately benign-leaning
SaProt	LLR -5.83	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	GERP -2.8
Regional constraint	o/e 1.05	unconstrained · MANE · 10 kb · p 0.39 · regional, not allelic
Overall
CADD	2.594	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

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: COQ7
Protein: p.Ser22Pro
Coding: c.64T>C
MANE Select: NM_016138
Type: single nucleotide variant
Location: chr16:19067728 (GRCh38)
Gene constraint: LOEUF 1.247 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.17 · 2 PDB
Residue 22: the 'required for nuclear localization' region

Full COQ7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COQ7 p.Ser22Phe Uncertain significance ★ ⚠ same residue
COQ7 p.Ser22= Likely benign ★ same residue
COQ7 p.Ser22Leu Uncertain significance ★ same residue
COQ7 c.367+5G>A Uncertain significance ★★ same type
COQ7 p.Ala140Val Uncertain significance ★★ ⚠ same type
COQ7 p.Ala19Ser Uncertain significance ★★ ⚠ same type
COQ7 p.Ala19Thr Uncertain significance ★★ ⚠ same type
COQ7 p.Ala68Gly 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/coq7-p-ser22pro (accessed [today's date]).

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