Is DKC1 p.Lys46= (c.138G>A) pathogenic?

DKC1 p.Lys46= (c.138G>A) is classified Benign in DKC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-31). Ultra-rare (popmax 0.0633%, sas); Associated with dyskeratosis congenita.

What condition is associated with DKC1 p.Lys46= (c.138G>A)?

DKC1 p.Lys46= (c.138G>A) is associated with dyskeratosis congenita (ClinVar).

How common is DKC1 p.Lys46= (c.138G>A) in the general population?

DKC1 p.Lys46= (c.138G>A) is ultra-rare (popmax 0.0633%, sas) (gnomAD).

How is Dyskeratosis congenita inherited?

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

DKC1 p.Lys46=

c.138G>A · rs369777662 · VCV1600369

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0633%, sas)

Conditions

dyskeratosis congenita

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.072	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	GERP 3, phastCons 0.94
Overall
CADD	8.706	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0633% South Asian · 36/56,833 alleles

Filtering AF 0.047% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0413%

Overall 0.00381% 46/1,207,830 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0633%	1,579
Remaining individualsnot grpmax-eligible	0.0147%	6,789
European (non-Finnish)	0.000336%	297,549

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
Protein: p.Lys46=
Coding: c.138G>A
MANE Select: NM_001363
dbSNP: rs369777662
Type: single nucleotide variant
Location: chrX:154765497 (GRCh38)
Structure: AlphaFold pLDDT 79.74 · 7 PDB

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.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
DKC1 p.Ala162Thr 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-lys46 (accessed [today's date]).

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