Is DNAJC5 p.Pro152= (c.456C>T) pathogenic?

DNAJC5 p.Pro152= (c.456C>T) is classified Benign/Likely benign in DNAJC5 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-11). Rare (popmax 0.432%, afr); Associated with Inborn genetic diseases.

What condition is associated with DNAJC5 p.Pro152= (c.456C>T)?

DNAJC5 p.Pro152= (c.456C>T) is associated with Inborn genetic diseases, neuronal ceroid lipofuscinosis (ClinVar).

How common is DNAJC5 p.Pro152= (c.456C>T) in the general population?

DNAJC5 p.Pro152= (c.456C>T) is rare (popmax 0.432%, afr) (gnomAD).

DNAJC5 p.Pro152=

c.456C>T · rs140326040 · VCV205368

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.432%, 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 -20	GERP -4.3
Overall
CADD	0.193	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.432% African / African-American · 324/75,060 alleles

Filtering AF 0.393% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.378%

Overall 0.024% 387/1,614,090 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.432%	232
Admixed American	0.0383%	2,610
Remaining individualsnot grpmax-eligible	0.0224%	4,465
Middle Eastern	0.0165%	6,058
South Asian	0.00439%	22,772
European (non-Finnish)	0.00178%	56,193

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.Pro152=
Coding: c.456C>T
MANE Select: NM_025219
dbSNP: rs140326040
Type: single nucleotide variant
Location: chr20:63930985 (GRCh38)
Gene constraint: LOEUF 0.205 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 74.09 · 2 PDB

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: neuronal ceroid lipofuscinosis

Similar variants

DNAJC5 p.Pro152Ser Uncertain significance ★ ⚠ same residue
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
DNAJC5 p.Arg164Lys Uncertain significance ★★ ⚠ same condition
DNAJC5 p.Arg36Gln 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-pro152 (accessed [today's date]).

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