Is DCK p.Ala2Val (c.5C>T) pathogenic?

DCK p.Ala2Val (c.5C>T) is classified Uncertain significance in DCK (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-04). AlphaMissense: likely pathogenic (0.6587); Absent from gnomAD v4.1.

How common is DCK p.Ala2Val (c.5C>T) in the general population?

DCK p.Ala2Val (c.5C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DCK p.Ala2Val (c.5C>T)?

AlphaMissense predicts likely pathogenic (score 0.6587) — an in-silico prediction, not a clinical call.

DCK p.Ala2Val

c.5C>T · VCV4009753

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6587 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,612,538)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.6587	likely pathogenic
REVEL	0.588	indeterminate
SaProt	LLR -8.17	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP -0.27, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 29 kb · p 1 · regional, not allelic
Overall
CADD	24.1	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,612,538). 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: DCK
Protein: p.Ala2Val
Coding: c.5C>T
MANE Select: NM_000788
Type: single nucleotide variant
Location: chr4:70993840 (GRCh38)
Gene constraint: LOEUF 1.031 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.13 · 58 PDB

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

Similar variants

DCK p.Asn39Ser Uncertain significance ★ ⚠ same type
DCK p.Asn60Ser Uncertain significance ★ ⚠ same type
DCK p.Asp160Asn Uncertain significance ★ ⚠ same type
DCK p.Asp160Val Uncertain significance ★ ⚠ same type
DCK p.Ile154Val Uncertain significance ★ ⚠ same type
DCK p.Ile189Leu Uncertain significance ★ ⚠ same type
DCK p.Ile233Val Uncertain significance ★ ⚠ same type
DCK p.Leu116Ile 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/dck-p-ala2val (accessed [today's date]).

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