Is COQ2 p.Pro103Leu (c.308C>T) pathogenic?

COQ2 p.Pro103Leu (c.308C>T) is classified Uncertain significance in COQ2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-06). AlphaMissense: likely benign (0.2441); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with COQ2 p.Pro103Leu (c.308C>T)?

COQ2 p.Pro103Leu (c.308C>T) is associated with Inborn genetic diseases (ClinVar).

How common is COQ2 p.Pro103Leu (c.308C>T) in the general population?

COQ2 p.Pro103Leu (c.308C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about COQ2 p.Pro103Leu (c.308C>T)?

AlphaMissense predicts likely benign (score 0.2441) — an in-silico prediction, not a clinical call.

COQ2 p.Pro103Leu

c.308C>T · rs2529770418 · VCV2299848

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2441 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2441	likely benign
REVEL	0.642	indeterminate
SaProt	LLR -14.80	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.7	GERP 0.51, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 21 kb · p 0.51 · regional, not allelic
Overall
CADD	24.6	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: COQ2
Protein: p.Pro103Leu
Coding: c.308C>T
MANE Select: NM_001358921
dbSNP: rs2529770418
Type: single nucleotide variant
Location: chr4:83279060 (GRCh38)
Gene constraint: LOEUF 1.032 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 85.64

Full COQ2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

COQ2 c.-4C>A Uncertain significance ★★ same condition
COQ2 p.Ala14Ser Uncertain significance ★★ same condition
COQ2 p.Ala28Glu Uncertain significance ★★ same condition
COQ2 p.Ala309Ser Uncertain significance ★★ ⚠ same condition
COQ2 p.Ala30Val Uncertain significance ★★ ⚠ same condition
COQ2 p.Ala35Gly Uncertain significance ★★ ⚠ same condition
COQ2 p.Ala37Val Uncertain significance ★★ ⚠ same condition
COQ2 p.Ala62Val Uncertain significance ★★ ⚠ same condition

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/coq2-p-pro103leu (accessed [today's date]).

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