Is COQ7 p.Pro17= (c.51G>A) pathogenic?

COQ7 p.Pro17= (c.51G>A) is classified Benign in COQ7 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-04). Common (popmax 22.5%, amr) — too common for a highly-penetrant pathogenic allele.

COQ7 p.Pro17=

Q: How common is COQ7 p.Pro17= (c.51G>A) in the general population?

COQ7 p.Pro17= (c.51G>A) is common (popmax 22.5%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.51G>A · rs17357834 · VCV669700

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 22.5%, amr) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.6	GERP -3.7
Overall
CADD	4.632	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 22.5% Admixed American · 13,111/58,378 alleles

Filtering AF 22.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 22%

Overall 18.1% 291,304/1,606,028 alleles · common exomes 264,167/1,453,822 · genomes 27,137/152,206 · joint denominator

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	36.3%	3
Admixed Americangrpmax	22.5%	4
Finnishnot grpmax-eligible	21.1%	5
European (non-Finnish)	18.9%	5
Ashkenazi Jewishnot grpmax-eligible	18.1%	6
Remaining individualsnot grpmax-eligible	17.2%	6
East Asian	14.8%	7
African / African-American	14.3%	7
Middle Eastern	12.9%	8
South Asian	9.42%	11

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: COQ7
Protein: p.Pro17=
Coding: c.51G>A
MANE Select: NM_016138
dbSNP: rs17357834
Type: single nucleotide variant
Location: chr16:19067715 (GRCh38)
Gene constraint: LOEUF 1.247 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.17 · 2 PDB
Residue 17: the 'required for nuclear localization' region

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

Similar variants

COQ7 p.Pro17Leu Benign/Likely benign ★★ 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
COQ7 p.Ala8Val Uncertain significance ★★ ⚠ same type
COQ7 p.Arg35His 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-pro17 (accessed [today's date]).

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