Is DNAJC1 p.Ser6Phe (c.17C>T) pathogenic?

DNAJC1 p.Ser6Phe (c.17C>T) is classified Uncertain significance in DNAJC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-06). AlphaMissense: likely benign (0.0816); Absent from gnomAD v4.1.

How common is DNAJC1 p.Ser6Phe (c.17C>T) in the general population?

DNAJC1 p.Ser6Phe (c.17C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DNAJC1 p.Ser6Phe (c.17C>T)?

AlphaMissense predicts likely benign (score 0.0816) — an in-silico prediction, not a clinical call.

DNAJC1 p.Ser6Phe

c.17C>T · VCV3841480

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0816 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,368,202)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0816	likely benign
REVEL	0.103	moderately benign-leaning
SaProt	LLR -8.60	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.45	GERP 1.2, phastCons 0.021
Regional constraint	o/e 1.02	unconstrained · MANE · 247 kb · p 0.65 · regional, not allelic
Overall
CADD	13.23	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,368,202). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DNAJC1
Protein: p.Ser6Phe
Coding: c.17C>T
MANE Select: NM_022365
Type: single nucleotide variant
Location: chr10:22003418 (GRCh38)
Gene constraint: LOEUF 0.961 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.45 · 2 PDB

Full DNAJC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAJC1 p.Ala263Ser Uncertain significance ★ ⚠ same type
DNAJC1 p.Ala3Thr Uncertain significance ★ ⚠ same type
DNAJC1 p.Ala417Gly Uncertain significance ★ ⚠ same type
DNAJC1 p.Ala455Val Uncertain significance ★ ⚠ same type
DNAJC1 p.Ala490Gly Uncertain significance ★ ⚠ same type
DNAJC1 p.Ala524Ser Uncertain significance ★ ⚠ same type
DNAJC1 p.Ala537Thr Uncertain significance ★ ⚠ same type
DNAJC1 p.Arg107Thr 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/dnajc1-p-ser6phe (accessed [today's date]).

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