DKC1 p.Ile7=
c.21T>A · rs1603429384 · VCV756357
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.65 | GERP 2.6, phastCons 0.001 |
| Overall | ||
| CADD | 5.181 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- DKC1
- Protein
- p.Ile7=
- Coding
- c.21T>A
- MANE Select
- NM_001363
- dbSNP
- rs1603429384
- Type
- single nucleotide variant
- Location
- chrX:154764903 (GRCh38)
- Structure
- AlphaFold pLDDT 79.74 · 7 PDB
- Residue 7
- the 'nucleolar localization' region
Similar variants
- DKC1 p.Ile7Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-p-ile7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown