Is DNAJC5 p.Ile171= (c.513C>T) pathogenic?

DNAJC5 p.Ile171= (c.513C>T) is classified Likely benign in DNAJC5 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-01-27). Ultra-rare (popmax 0.0174%, sas); Associated with Inborn genetic diseases.

What condition is associated with DNAJC5 p.Ile171= (c.513C>T)?

DNAJC5 p.Ile171= (c.513C>T) is associated with Inborn genetic diseases, neuronal ceroid lipofuscinosis (ClinVar).

How common is DNAJC5 p.Ile171= (c.513C>T) in the general population?

DNAJC5 p.Ile171= (c.513C>T) is ultra-rare (popmax 0.0174%, sas) (gnomAD).

DNAJC5 p.Ile171=

c.513C>T · rs745794091 · VCV588981

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0174%, sas)

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 -1.3	GERP -3, phastCons 0.001
Overall
CADD	9.511	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0174% South Asian · 15/86,112 alleles

Filtering AF 0.0107% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00866%

Overall 0.00183% 26/1,419,154 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0174%	5,741
Remaining individualsnot grpmax-eligible	0.00327%	30,580
East Asian	0.00234%	42,650
European (non-Finnish)	0.000687%	145,524

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.Ile171=
Coding: c.513C>T
MANE Select: NM_025219
dbSNP: rs745794091
Type: single nucleotide variant
Location: chr20:63931484 (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.Ile171Ser 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-ile171 (accessed [today's date]).

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