Is DKC1 p.Lys499Arg (c.1496A>G) pathogenic?

DKC1 p.Lys499Arg (c.1496A>G) is classified Uncertain significance in DKC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-02). AlphaMissense: likely benign (0.0913); Very rare (popmax 0.00034%, nfe); Associated with dyskeratosis congenita, X-linked.

What condition is associated with DKC1 p.Lys499Arg (c.1496A>G)?

DKC1 p.Lys499Arg (c.1496A>G) is associated with dyskeratosis congenita, X-linked (ClinVar).

How common is DKC1 p.Lys499Arg (c.1496A>G) in the general population?

DKC1 p.Lys499Arg (c.1496A>G) is very rare (popmax 0.00034%, nfe) (gnomAD).

What do computational predictors say about DKC1 p.Lys499Arg (c.1496A>G)?

AlphaMissense predicts likely benign (score 0.0913) — an in-silico prediction, not a clinical call.

DKC1 p.Lys499Arg

c.1496A>G · rs1358702646 · VCV3254578

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0913 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00034%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

dyskeratosis congenita, X-linked

Computational evidence

Protein change
AlphaMissense	0.0913	likely benign
REVEL	0.353	indeterminate
SaProt	LLR -9.52	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7	GERP 3.6, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 1,637 bp · p 0.19 · regional, not allelic
Overall
CADD	20.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00034% European (non-Finnish) · 3/881,906 alleles

Filtering AF 9.1e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.5e-05%

Overall 0.000252% 3/1,191,617 alleles · very rare

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.Lys499Arg
Coding: c.1496A>G
MANE Select: NM_001363
dbSNP: rs1358702646
Type: single nucleotide variant
Location: chrX:154776818 (GRCh38)
Structure: AlphaFold pLDDT 79.74 · 7 PDB
Residue 499: the 'disordered' region; the 'nuclear and nucleolar localization' region

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

Disease context

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

Similar variants

DKC1 p.Ala353Val Pathogenic ★★ ⚠ same condition
DKC1 p.Ile38Met Likely pathogenic ★★ ⚠ same condition
DKC1 p.Thr49Met Pathogenic ★★ ⚠ same condition
DKC1 p.Thr66Ala Pathogenic/Likely pathogenic ★★ ⚠ same condition
DKC1 p.Gln414Glu Uncertain significance ★★ ⚠ same condition
DKC1 p.Glu440Lys Uncertain significance ★★ ⚠ same condition
DKC1 p.Ile163Leu Uncertain significance ★★ ⚠ same condition
DKC1 p.Ile187Leu 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-lys499arg (accessed [today's date]).

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