Is DNAJC5 p.Pro44= (c.132C>T) pathogenic?

DNAJC5 p.Pro44= (c.132C>T) is classified Benign/Likely benign in DNAJC5 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-01-13). Low-frequency (popmax 1.04%, afr); Associated with Inborn genetic diseases.

What condition is associated with DNAJC5 p.Pro44= (c.132C>T)?

DNAJC5 p.Pro44= (c.132C>T) is associated with Inborn genetic diseases, ceroid lipofuscinosis, neuronal, 4 (Kufs type), neuronal ceroid lipofuscinosis (ClinVar).

How common is DNAJC5 p.Pro44= (c.132C>T) in the general population?

DNAJC5 p.Pro44= (c.132C>T) is low-frequency (popmax 1.04%, afr) (gnomAD).

DNAJC5 p.Pro44=

c.132C>T · rs140948457 · VCV205366

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.04%, afr)

Conditions

Inborn genetic diseases

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 -6.6	GERP -4.1
Overall
CADD	6.583	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.04% African / African-American · 777/75,016 alleles

Filtering AF 0.975% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.951%

Overall 0.0532% 859/1,613,998 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.04%	97
Remaining individualsnot grpmax-eligible	0.0496%	2,016
Admixed American	0.0317%	3,158
East Asian	0.0223%	4,485
South Asian	0.0022%	45,542
European (non-Finnish)	0.00169%	58,999

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: DNAJC5
Protein: p.Pro44=
Coding: c.132C>T
MANE Select: NM_025219
dbSNP: rs140948457
Type: single nucleotide variant
Location: chr20:63929336 (GRCh38)
Gene constraint: LOEUF 0.205 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 74.09 · 2 PDB
Residue 44: the j domain; a turn

Full DNAJC5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: ceroid lipofuscinosis, neuronal, 4 (Kufs type)neuronal ceroid lipofuscinosis

Similar variants

DNAJC5 p.Leu115Arg Pathogenic ★★ same condition
DNAJC5 c.-109A>G Uncertain significance ★★ same condition
DNAJC5 c.-11-2A>G Uncertain significance ★★ same condition
DNAJC5 p.Ala176Val Uncertain significance ★★ ⚠ same condition
DNAJC5 p.Ala26Thr Uncertain significance ★★ ⚠ same condition
DNAJC5 p.Ala54Thr Uncertain significance ★★ ⚠ same condition
DNAJC5 p.Ala54Val Uncertain significance ★★ ⚠ same condition
DNAJC5 p.Ala63Thr 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/dnajc5-p-pro44 (accessed [today's date]).

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