DNAJC6 p.Asp352=
c.1056C>T · VCV3905308
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00212%, nfe)
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 -0.95 | GERP -4.2, phastCons 0.005 |
| Overall | ||
| CADD | 8.684 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00212%
European (non-Finnish) · 25/1,180,008 alleles
Filtering AF
0.00145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00123%
Overall
0.00173%
28/1,613,980 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00212% | 47,200 |
| Admixed American | 0.00167% | 59,986 |
| Finnishnot grpmax-eligible | 0.00156% | 64,026 |
| African / African-American | 0.00134% | 74,898 |
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
- DNAJC6
- Protein
- p.Asp352=
- Coding
- c.1056C>T
- MANE Select
- NM_001256864
- Type
- single nucleotide variant
- Location
- chr1:65386872 (GRCh38)
- Gene constraint
- LOEUF 0.416 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.29
- Residue 352
- the c2 tensin-type domain
Similar variants
- DNAJC6 p.Arg330Ter Pathogenic ★★ same type
- DNAJC6 p.Ala226Val Uncertain significance ★★ ⚠ same type
- DNAJC6 p.Ala234Thr Uncertain significance ★★ ⚠ same type
- DNAJC6 p.Ala277Thr Uncertain significance ★★ ⚠ same type
- DNAJC6 p.Ala611Val Uncertain significance ★★ ⚠ same type
- DNAJC6 p.Ala626Val Uncertain significance ★★ ⚠ same type
- DNAJC6 p.Ala770Val Uncertain significance ★★ ⚠ same type
- DNAJC6 p.Ala836Ser 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/dnajc6-p-asp352 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown