Is COMTD1 p.Glu189Lys (c.565G>A) pathogenic?

COMTD1 p.Glu189Lys (c.565G>A) is classified Uncertain significance in COMTD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-02). AlphaMissense: likely benign (0.122); Very rare (popmax 0.000343%, nfe).

How common is COMTD1 p.Glu189Lys (c.565G>A) in the general population?

COMTD1 p.Glu189Lys (c.565G>A) is very rare (popmax 0.000343%, nfe) (gnomAD).

What do computational predictors say about COMTD1 p.Glu189Lys (c.565G>A)?

AlphaMissense predicts likely benign (score 0.122) — an in-silico prediction, not a clinical call.

COMTD1 p.Glu189Lys

c.565G>A · rs769912092 · VCV2240312

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.122 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000343%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.122	likely benign
REVEL	0.088	moderately benign-leaning
SaProt	LLR -9.35	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 4.8	GERP 1, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 1,852 bp · p 0.73 · regional, not allelic
Overall
CADD	19.2	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

Grpmax group 0.000343% European (non-Finnish) · 4/1,167,854 alleles

Filtering AF 8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000279% 4/1,435,308 alleles · very rare

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: COMTD1
Protein: p.Glu189Lys
Coding: c.565G>A
MANE Select: NM_144589
dbSNP: rs769912092
Type: single nucleotide variant
Location: chr10:75234681 (GRCh38)
Gene constraint: LOEUF 1.869 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.67 · 1 PDB

Full COMTD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COMTD1 p.Ala126Thr Uncertain significance ★ ⚠ same type
COMTD1 p.Ala126Val Uncertain significance ★ ⚠ same type
COMTD1 p.Ala186Thr Uncertain significance ★ ⚠ same type
COMTD1 p.Ala91Gly Uncertain significance ★ ⚠ same type
COMTD1 p.Arg129Leu Uncertain significance ★ ⚠ same type
COMTD1 p.Arg129Pro Uncertain significance ★ ⚠ same type
COMTD1 p.Arg144Trp Uncertain significance ★ ⚠ same type
COMTD1 p.Arg212Lys 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/comtd1-p-glu189lys (accessed [today's date]).

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