DKC1 p.Leu511=
c.1531T>C · rs781861230 · VCV2888788
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
dyskeratosis congenita
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 0.86 | GERP -2.9, phastCons 0.002 |
| Overall | ||
| CADD | 5.206 | 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.Leu511=
- Coding
- c.1531T>C
- MANE Select
- NM_001363
- dbSNP
- rs781861230
- Type
- single nucleotide variant
- Location
- chrX:154776853 (GRCh38)
- Structure
- AlphaFold pLDDT 79.74 · 7 PDB
- Residue 511
- the 'disordered' region; the 'nuclear and nucleolar localization' region
Disease context
dyskeratosis congenita — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Dyskeratosis congenita (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive, X-linked recessive
- Onset
- Adolescent, Adult, Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 1 000 000 (Europe)
Similar variants
- DKC1 p.Leu511Phe Likely benign ★ ⚠ same residue
- DKC1 p.Ala353Val Pathogenic ★★ ⚠ same condition
- DKC1 p.Asn63Lys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- DKC1 p.Thr49Met Pathogenic ★★ ⚠ same condition
- DKC1 p.Thr66Ala Pathogenic/Likely pathogenic ★★ ⚠ same condition
- DKC1 c.1339-10T>G Uncertain significance ★★ same condition
- DKC1 c.16+5G>A Uncertain significance ★★ same condition
- DKC1 c.640+3G>A Uncertain significance ★★ same condition
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-leu511 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown