Is DNAJB1 p.Phe106= (c.318C>T) pathogenic?

DNAJB1 p.Phe106= (c.318C>T) is classified Likely benign in DNAJB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-11). Ultra-rare (popmax 0.0164%, mid).

How common is DNAJB1 p.Phe106= (c.318C>T) in the general population?

DNAJB1 p.Phe106= (c.318C>T) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

DNAJB1 p.Phe106=

c.318C>T · rs777046843 · VCV758224

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

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 -2	GERP -2.4
Overall
CADD	9.107	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,084 alleles

Filtering AF 0.00114% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000971%

Overall 0.00161% 26/1,613,642 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,084
Admixed American	0.00333%	29,990
European (non-Finnish)	0.00178%	56,191
Remaining individualsnot grpmax-eligible	0.0016%	62,478
African / African-American	0.00134%	74,894

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: DNAJB1
Protein: p.Phe106=
Coding: c.318C>T
MANE Select: NM_006145
dbSNP: rs777046843
Type: single nucleotide variant
Location: chr19:14516940 (GRCh38)
Gene constraint: LOEUF 0.953 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.71 · 15 PDB

Full DNAJB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAJB1 p.Asn272= Benign ★★ same type
DNAJB1 p.Val288= Benign ★★ same type
DNAJB1 p.Ala265Val Uncertain significance ★ ⚠ same type
DNAJB1 p.Arg119Gln Uncertain significance ★ ⚠ same type
DNAJB1 p.Arg13Cys Uncertain significance ★ ⚠ same type
DNAJB1 p.Arg26Leu Uncertain significance ★ ⚠ same type
DNAJB1 p.Arg290Ser Uncertain significance ★ ⚠ same type
DNAJB1 p.Arg294Trp 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/dnajb1-p-phe106 (accessed [today's date]).

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