DKC1 c.*40T>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.8%, 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 -5.6 | GERP -6.9 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 0.288 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.8%
African / African-American · 1,522/54,388 alleles
Filtering AF
2.68%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.63%
Overall
0.157%
1,681/1,071,172 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.8% | 36 |
| Remaining individualsnot grpmax-eligible | 0.173% | 577 |
| Admixed American | 0.169% | 590 |
| Middle Eastern | 0.05% | 2,002 |
| South Asian | 0.0118% | 8,456 |
| European (non-Finnish) | 0.00115% | 86,939 |
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
- DKC1
- Coding
- c.*40T>C
- MANE Select
- NM_001363
- dbSNP
- rs143263287
- Type
- single nucleotide variant
- Location
- chrX:154776907 (GRCh38)
- Structure
- AlphaFold pLDDT 79.74 · 7 PDB
Similar variants
- DKC1 p.Ala353Val Pathogenic ★★ ⚠ same type
- DKC1 p.Asn63Lys Pathogenic/Likely pathogenic ★★ ⚠ same type
- DKC1 p.Ile38Met Likely pathogenic ★★ ⚠ same type
- DKC1 p.Thr49Met Pathogenic ★★ ⚠ same type
- DKC1 p.Thr66Ala Pathogenic/Likely pathogenic ★★ ⚠ same type
- DKC1 c.1339-10T>G Uncertain significance ★★ same type
- DKC1 c.16+5G>A Uncertain significance ★★ same type
- DKC1 c.640+3G>A 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/dkc1-c-star-40t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown