Is DNAJC7 p.Ala4Val (c.11C>T) pathogenic?

DNAJC7 p.Ala4Val (c.11C>T) is classified Uncertain significance in DNAJC7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-06). AlphaMissense: likely benign (0.1794); Absent from gnomAD v4.1.

How common is DNAJC7 p.Ala4Val (c.11C>T) in the general population?

DNAJC7 p.Ala4Val (c.11C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DNAJC7 p.Ala4Val (c.11C>T)?

AlphaMissense predicts likely benign (score 0.1794) — an in-silico prediction, not a clinical call.

DNAJC7 p.Ala4Val

c.11C>T · VCV3504046

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1794 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,608,266)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1794	likely benign
REVEL	0.036	moderately benign-leaning
SaProt	LLR -7.03	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 9.7	GERP 1.8, phastCons 1
Regional constraint	o/e 1.17	unconstrained · MANE · 17 kb · p 0.22 · regional, not allelic
Overall
CADD	23.5	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 1,608,266). 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: DNAJC7
Protein: p.Ala4Val
Coding: c.11C>T
MANE Select: NM_003315
Type: single nucleotide variant
Location: chr17:42017406 (GRCh38)
Gene constraint: LOEUF 0.389 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 90.83

Full DNAJC7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAJC7 c.167-65C>A Benign ★★ same type
DNAJC7 c.406-8C>T Benign ★★ same type
DNAJC7 c.599+161G>A Benign ★★ same type
DNAJC7 p.Pro193= Benign ★★ same type
DNAJC7 p.Ala115Pro Uncertain significance ★ ⚠ same type
DNAJC7 p.Ala141Thr Uncertain significance ★ ⚠ same type
DNAJC7 p.Ala370Val Uncertain significance ★ ⚠ same type
DNAJC7 p.Arg117His 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/dnajc7-p-ala4val (accessed [today's date]).

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