Is DNAJB11 p.Val20= (c.60G>A) pathogenic?

DNAJB11 p.Val20= (c.60G>A) is classified Uncertain significance in DNAJB11 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-25). Very rare (popmax 0.00139%, afr).

How common is DNAJB11 p.Val20= (c.60G>A) in the general population?

DNAJB11 p.Val20= (c.60G>A) is very rare (popmax 0.00139%, afr) (gnomAD).

DNAJB11 p.Val20=

c.60G>A · rs1446145842 · VCV2419130

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00139%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.34	donor gain · deltas
Pangolin	Δ0.22	gain · loss 0.03 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 3.8	GERP 0.93, phastCons 1
Overall
CADD	14.1	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00139% African / African-American · 1/72,086 alleles

Filtering AF 8.4e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.7e-05%

Overall 0.000398% 6/1,508,884 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.00178%	56,042
African / African-Americangrpmax	0.00139%	72,086
European (non-Finnish)	0.000359%	278,503

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: DNAJB11
Protein: p.Val20=
Coding: c.60G>A
MANE Select: NM_016306
dbSNP: rs1446145842
Type: single nucleotide variant
Location: chr3:186570957 (GRCh38)
Gene constraint: LOEUF 0.933 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.34

Full DNAJB11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAJB11 p.Arg206Ter Pathogenic ★★ same type
DNAJB11 p.Arg242Ter Pathogenic ★★ same type
DNAJB11 p.Arg24Ter Pathogenic ★★ same type
DNAJB11 p.Arg34Ter Pathogenic ★★ same type
DNAJB11 p.Glu144Ter Pathogenic/Likely pathogenic ★★ same type
DNAJB11 p.Leu77Pro Likely pathogenic ★★ same type
DNAJB11 p.Pro54Arg Likely pathogenic ★★ same type
DNAJB11 p.Ala297Val 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/dnajb11-p-val20 (accessed [today's date]).

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