Is DNAJB13 p.Ser36Ala (c.106T>G) pathogenic?

DNAJB13 p.Ser36Ala (c.106T>G) is classified Uncertain significance in DNAJB13 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-12-02). AlphaMissense: likely benign (0.0897); Ultra-rare (popmax 0.0161%, nfe); Associated with primary ciliary dyskinesia.

What condition is associated with DNAJB13 p.Ser36Ala (c.106T>G)?

DNAJB13 p.Ser36Ala (c.106T>G) is associated with primary ciliary dyskinesia (ClinVar).

How common is DNAJB13 p.Ser36Ala (c.106T>G) in the general population?

DNAJB13 p.Ser36Ala (c.106T>G) is ultra-rare (popmax 0.0161%, nfe) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

What do computational predictors say about DNAJB13 p.Ser36Ala (c.106T>G)?

AlphaMissense predicts likely benign (score 0.0897) — an in-silico prediction, not a clinical call.

DNAJB13 p.Ser36Ala

c.106T>G · rs144741417 · VCV977601

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0897 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0161%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

primary ciliary dyskinesia

Computational evidence

Protein change
AlphaMissense	0.0897	likely benign
REVEL	0.07	moderately benign-leaning
SaProt	LLR -10.78	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2	GERP -4.2, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 19 kb · p 0.47 · regional, not allelic
Overall
CADD	13.03	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 0.0161% European (non-Finnish) · 190/1,180,034 alleles

Filtering AF 0.0142% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0134%

Overall 0.0125% 202/1,613,966 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0161%	6,211
Remaining individualsnot grpmax-eligible	0.0096%	10,415
African / African-American	0.00668%	14,977
Admixed American	0.00167%	59,986

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: DNAJB13
Protein: p.Ser36Ala
Coding: c.106T>G
MANE Select: NM_153614
dbSNP: rs144741417
Type: single nucleotide variant
Location: chr11:73958354 (GRCh38)
Gene constraint: LOEUF 0.9 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.81 · 1 PDB
Residue 36: the j domain

Full DNAJB13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Primary ciliary dyskinesia (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Neonatal
Prevalence: 1-5 / 10 000 (Pakistan)

Similar variants

DNAJB13 p.Ser36Pro Uncertain significance ★ same residue
DNAJB13 p.Gln136Ter Pathogenic/Likely pathogenic ★★ same type
DNAJB13 p.Arg131Gln Uncertain significance ★★ ⚠ same type
DNAJB13 p.Arg142Gln Uncertain significance ★★ ⚠ same type
DNAJB13 p.Arg222Cys Uncertain significance ★★ ⚠ same type
DNAJB13 p.Arg301Cys Uncertain significance ★★ ⚠ same type
DNAJB13 p.Asn14Asp Uncertain significance ★★ ⚠ same type
DNAJB13 p.Asp169Gly 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/dnajb13-p-ser36ala (accessed [today's date]).

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