Is DOK7 p.Pro29Ala (c.85C>G) pathogenic?

DOK7 p.Pro29Ala (c.85C>G) is classified Uncertain significance in DOK7 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-19). AlphaMissense: likely pathogenic (0.6464); Very rare (popmax 0.006%, nfe); Associated with fetal akinesia deformation sequence 1.

What condition is associated with DOK7 p.Pro29Ala (c.85C>G)?

DOK7 p.Pro29Ala (c.85C>G) is associated with fetal akinesia deformation sequence 1, congenital myasthenic syndrome 10 (ClinVar).

How common is DOK7 p.Pro29Ala (c.85C>G) in the general population?

DOK7 p.Pro29Ala (c.85C>G) is very rare (popmax 0.006%, nfe) (gnomAD).

What do computational predictors say about DOK7 p.Pro29Ala (c.85C>G)?

AlphaMissense predicts likely pathogenic (score 0.6464) — an in-silico prediction, not a clinical call.

DOK7 p.Pro29Ala

c.85C>G · rs902383987 · VCV1925847

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6464 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.006%, nfe)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

fetal akinesia deformation sequence 1

Computational evidence

Protein change
AlphaMissense	0.6464	likely pathogenic
REVEL	0.382	indeterminate
SaProt	LLR -11.90	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5	GERP 0.65, phastCons 1
Regional constraint	o/e 1.44	unconstrained · MANE · 30 kb · p 2.5e-31 · regional, not allelic
Overall
CADD	26.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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 0.006% European (non-Finnish) · 68/1,132,392 alleles

Filtering AF 0.00481% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0044%

Overall 0.00457% 69/1,509,416 alleles · very rare exomes 68/1,361,586 · genomes 1/147,830 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.006%	16,653
Remaining individualsnot grpmax-eligible	0.00171%	58,646

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: DOK7
Protein: p.Pro29Ala
Coding: c.85C>G
MANE Select: NM_173660
dbSNP: rs902383987
Type: single nucleotide variant
Location: chr4:3463536 (GRCh38)
Gene constraint: LOEUF 1.658 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.61
Residue 29: the ph domain

Full DOK7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

fetal akinesia deformation sequence 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: congenital myasthenic syndrome 10

Similar variants

DOK7 p.Pro29Leu Uncertain significance ★ ⚠ same residue
DOK7 p.Pro29= Likely benign ★ same residue
DOK7 p.Pro29Gln Uncertain significance ★ ⚠ same residue
DOK7 c.331+1G>T Pathogenic ★★ same condition
DOK7 c.332-1G>A Likely pathogenic ★★ same condition
DOK7 c.332-1G>C Likely pathogenic ★★ same condition
DOK7 c.332-1G>T Likely pathogenic ★★ same condition
DOK7 p.Arg158Gln Pathogenic/Likely pathogenic ★★ 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/dok7-p-pro29ala (accessed [today's date]).

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