DNAJC6 c.666+239A>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 64.2%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +239 | deep intronic (+239 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.93 | GERP 2.9 |
| Non-coding constraint | Z 0.75 | 1 kb window · o/e 0.93 · regional · uncalibrated |
| Overall | ||
| CADD | 8.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
64.2%
East Asian · 13,984/21,774 alleles
Filtering AF
63.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 63%
Overall
19.3%
79,352/411,690 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 64.2% | 2 |
| African / African-American | 55.6% | 2 |
| South Asian | 31.4% | 3 |
| Admixed American | 26.3% | 4 |
| Middle Eastern | 18.7% | 5 |
| Remaining individualsnot grpmax-eligible | 17.7% | 6 |
| Ashkenazi Jewishnot grpmax-eligible | 16.8% | 6 |
| Finnishnot grpmax-eligible | 15.7% | 6 |
| European (non-Finnish) | 6.65% | 15 |
| Amishnot grpmax-eligible | 6.47% | 15 |
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
- Coding
- c.666+239A>C
- MANE Select
- NM_001256864
- dbSNP
- rs1408994
- Type
- single nucleotide variant
- Location
- chr1:65379763 (GRCh38)
- Gene constraint
- LOEUF 0.416 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.29
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-c-666-plus-239a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown