DNAJC16 p.Ser560=
c.1680C>T · rs148700636 · VCV2594342
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0615%, afr)
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 -0.97 | GERP -3.9, phastCons 0.006 |
| Overall | ||
| CADD | 7.696 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0615%
African / African-American · 46/74,740 alleles
Filtering AF
0.0473%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0424%
Overall
0.0057%
92/1,613,076 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0615% | 1,625 |
| Admixed American | 0.00838% | 11,939 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,493 |
| East Asian | 0.00446% | 22,429 |
| European (non-Finnish) | 0.0028% | 35,752 |
| Finnishnot grpmax-eligible | 0.00156% | 64,000 |
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
- DNAJC16
- Protein
- p.Ser560=
- Coding
- c.1680C>T
- MANE Select
- NM_015291
- dbSNP
- rs148700636
- Type
- single nucleotide variant
- Location
- chr1:15566082 (GRCh38)
- Gene constraint
- LOEUF 0.933 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.54
Similar variants
- DNAJC16 p.Ala337Gly Uncertain significance ★ ⚠ same type
- DNAJC16 p.Ala53Ser Uncertain significance ★ ⚠ same type
- DNAJC16 p.Ala53Thr Uncertain significance ★ ⚠ same type
- DNAJC16 p.Ala95Thr Uncertain significance ★ ⚠ same type
- DNAJC16 p.Arg111His Uncertain significance ★ ⚠ same type
- DNAJC16 p.Arg113His Uncertain significance ★ ⚠ same type
- DNAJC16 p.Arg134Gln Uncertain significance ★ ⚠ same type
- DNAJC16 p.Arg204Lys 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/dnajc16-p-ser560 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown