Is DOK7 p.Ser462= (c.1386C>T) pathogenic?

DOK7 p.Ser462= (c.1386C>T) is classified Likely benign in DOK7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-03). Ultra-rare (popmax 0.0202%, sas); Associated with congenital myasthenic syndrome 10.

What condition is associated with DOK7 p.Ser462= (c.1386C>T)?

DOK7 p.Ser462= (c.1386C>T) is associated with congenital myasthenic syndrome 10, fetal akinesia deformation sequence 1 (ClinVar).

How common is DOK7 p.Ser462= (c.1386C>T) in the general population?

DOK7 p.Ser462= (c.1386C>T) is ultra-rare (popmax 0.0202%, sas) (gnomAD).

DOK7 p.Ser462=

c.1386C>T · rs776733631 · VCV1575624

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0202%, sas)

Conditions

congenital myasthenic syndrome 10

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 -4.1	GERP -1.8
Overall
CADD	4.37	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0202% South Asian · 18/89,110 alleles

Filtering AF 0.013% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0108%

Overall 0.00621% 99/1,595,000 alleles · ultra-rare exomes 91/1,442,790 · genomes 8/152,210 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0202%	4,951
East Asian	0.0136%	7,352
European (non-Finnish)	0.00563%	17,750
Remaining individualsnot grpmax-eligible	0.00487%	20,530
Admixed American	0.00349%	28,654
Finnishnot grpmax-eligible	0.00329%	30,396
African / African-American	0.00268%	37,296

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.Ser462=
Coding: c.1386C>T
MANE Select: NM_173660
dbSNP: rs776733631
Type: single nucleotide variant
Location: chr4:3493372 (GRCh38)
Gene constraint: LOEUF 1.658 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.61
Residue 462: the 'disordered' region

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

Disease context

congenital myasthenic syndrome 10 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: fetal akinesia deformation sequence 1

Similar variants

DOK7 p.Ser462Gly Uncertain significance ★ ⚠ same residue
DOK7 p.Ser462Thr 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
DOK7 p.Arg201Ter 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-ser462 (accessed [today's date]).

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