Is DNAJB6 p.Arg127Ser (c.381G>T) pathogenic?

DNAJB6 p.Arg127Ser (c.381G>T) is classified Uncertain significance in DNAJB6 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-01-01). AlphaMissense: ambiguous (0.5629); Very rare (popmax 0.00854%, amr); Associated with autosomal dominant limb-girdle muscular dystrophy type 1D (DNAJB6).

What condition is associated with DNAJB6 p.Arg127Ser (c.381G>T)?

DNAJB6 p.Arg127Ser (c.381G>T) is associated with autosomal dominant limb-girdle muscular dystrophy type 1D (DNAJB6) (ClinVar).

How common is DNAJB6 p.Arg127Ser (c.381G>T) in the general population?

DNAJB6 p.Arg127Ser (c.381G>T) is very rare (popmax 0.00854%, amr) (gnomAD).

How is DNAJB6-related limb-girdle muscular dystrophy D1 inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about DNAJB6 p.Arg127Ser (c.381G>T)?

AlphaMissense predicts ambiguous (score 0.5629) — an in-silico prediction, not a clinical call.

DNAJB6 p.Arg127Ser

c.381G>T · rs747600463 · VCV501446

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.5629 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00854%, amr)

Conditions

autosomal dominant limb-girdle muscular dystrophy type 1D (DNAJB6)

Computational evidence

Protein change
AlphaMissense	0.5629	ambiguous
REVEL	0.322	indeterminate
SaProt	LLR -6.52	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.3	GERP -4.1, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 49 kb · p 0.16 · regional, not allelic
Overall
CADD	18.9	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

Grpmax group 0.00854% Admixed American · 5/58,550 alleles

Filtering AF 0.00329% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00211%

Overall 0.000311% 5/1,608,930 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: DNAJB6
Protein: p.Arg127Ser
Coding: c.381G>T
MANE Select: NM_058246
dbSNP: rs747600463
Type: single nucleotide variant
Location: chr7:157382280 (GRCh38)
Gene constraint: LOEUF 0.92 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 64.04 · 4 PDB
Residue 127: the 'interaction with hsp70' region; the 'interaction with krt18' region

Full DNAJB6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autosomal dominant limb-girdle muscular dystrophy type 1D (DNAJB6) — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For DNAJB6-related limb-girdle muscular dystrophy D1 (Orphanet):

Inheritance: Autosomal dominant
Onset: Adult

Similar variants

DNAJB6 p.Arg127Gly Uncertain significance ★ same residue
DNAJB6 p.Phe89Ile Pathogenic ★★ same condition
DNAJB6 p.Phe91Leu Pathogenic ★★ same condition
DNAJB6 p.Phe91Val Pathogenic/Likely pathogenic ★★ same condition
DNAJB6 p.Pro96Arg Pathogenic ★★ same condition
DNAJB6 c.66-2A>G Uncertain significance ★★ same condition
DNAJB6 c.-7G>A Uncertain significance ★★ same condition
DNAJB6 p.Ala22Val 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/dnajb6-p-arg127ser (accessed [today's date]).

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