Is COX20 p.Cys29= (c.87C>T) pathogenic?

COX20 p.Cys29= (c.87C>T) is classified Benign/Likely benign in COX20 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-01). Ultra-rare (popmax 0.0912%, mid).

How common is COX20 p.Cys29= (c.87C>T) in the general population?

COX20 p.Cys29= (c.87C>T) is ultra-rare (popmax 0.0912%, mid) (gnomAD).

COX20 p.Cys29=

c.87C>T · rs140032239 · VCV377749

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0912%, mid)

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 1.5	GERP -0.4, phastCons 1
Overall
CADD	7.789	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0912% Middle Eastern · 5/5,482 alleles

Filtering AF 0.0608% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0592%

Overall 0.0573% 923/1,611,002 alleles · ultra-rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.304%	329
Middle Easterngrpmax	0.0912%	1,096
European (non-Finnish)	0.0646%	1,548
Remaining individualsnot grpmax-eligible	0.0577%	1,732
African / African-American	0.02%	4,995
Admixed American	0.0117%	8,564
Finnishnot grpmax-eligible	0.00782%	12,794
South Asian	0.0033%	30,289
East Asian	0.00223%	44,864

Ashkenazi Jewish 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: COX20
Protein: p.Cys29=
Coding: c.87C>T
MANE Select: NM_198076
dbSNP: rs140032239
Type: single nucleotide variant
Location: chr1:244841988 (GRCh38)
Gene constraint: LOEUF 1.927 · pLI 0.06 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 66.42

Full COX20 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COX20 c.157+3G>C Pathogenic/Likely pathogenic ★★ same type
COX20 p.Lys14Arg Pathogenic ★★ ⚠ same type
COX20 p.Tyr36Ter Likely pathogenic ★★ same type
COX20 p.Ala3Thr Uncertain significance ★★ ⚠ same type
COX20 p.Arg31Trp Uncertain significance ★★ ⚠ same type
COX20 p.Arg54Gly Uncertain significance ★★ ⚠ same type
COX20 p.Asp107Asn Uncertain significance ★★ ⚠ same type
COX20 p.Asp107His 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/cox20-p-cys29 (accessed [today's date]).

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