Is DKC1 p.Ala2del (c.5_7del) pathogenic?

DKC1 p.Ala2del (c.57del) is classified Pathogenic in DKC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-13). Absent from gnomAD; Associated with dyskeratosis congenita.

What condition is associated with DKC1 p.Ala2del (c.5_7del)?

DKC1 p.Ala2del (c.5_7del) is associated with dyskeratosis congenita (ClinVar).

How common is DKC1 p.Ala2del (c.5_7del) in the general population?

DKC1 p.Ala2del (c.5_7del) is absent from gnomAD (gnomAD).

How is Dyskeratosis congenita inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DKC1 p.Ala2del

c.5_7del · rs2523673228 · VCV2828899

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

dyskeratosis congenita

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.9	GERP 3.2, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DKC1
Protein: p.Ala2del
Coding: c.5_7del
MANE Select: NM_001363
dbSNP: rs2523673228
Type: Deletion
Location: chrX:154762968 (GRCh38)
Structure: AlphaFold pLDDT 79.74 · 7 PDB
Residue 2: a UniProt-annotated variant site (in dkcx); the 'nucleolar localization' region; a modified residue (n-acetylalanine)

Full DKC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

dyskeratosis congenita — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For 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.Ala2Val Conflicting classifications of pathogenicity ★ ⚠ same residue
DKC1 c.171+14del Benign/Likely benign ★★ same condition
DKC1 p.Leu37del Likely pathogenic ★ same condition
DKC1 c.1477-14_1477-11del Uncertain significance ★ same condition
DKC1 p.Glu18del Uncertain significance ★ same condition
DKC1 p.Glu426del Uncertain significance ★ same condition
DKC1 p.Val431_Glu440del Uncertain significance ★ same condition
DKC1 p.Val432del 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-ala2del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown