Is DCK p.Asp160Asn (c.478G>A) pathogenic?

DCK p.Asp160Asn (c.478G>A) is classified Uncertain significance in DCK (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-05). AlphaMissense: likely benign (0.0838); Absent from gnomAD v4.1.

How common is DCK p.Asp160Asn (c.478G>A) in the general population?

DCK p.Asp160Asn (c.478G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DCK p.Asp160Asn (c.478G>A)?

AlphaMissense predicts likely benign (score 0.0838) — an in-silico prediction, not a clinical call.

DCK p.Asp160Asn

c.478G>A · VCV3838543

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0838 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.0838	likely benign
REVEL	0.436	indeterminate
SaProt	LLR -6.44	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 9.7	GERP 1.9, phastCons 1
Regional constraint	o/e 0.43	unconstrained · MANE · 105 bp · p 0.00025 · regional, not allelic
Overall
CADD	23.3	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

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: DCK
Protein: p.Asp160Asn
Coding: c.478G>A
MANE Select: NM_000788
Type: single nucleotide variant
Location: chr4:71023635 (GRCh38)
Gene constraint: LOEUF 1.031 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.13 · 58 PDB
Residue 160: an α-helix

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

Similar variants

DCK p.Asp160Val Uncertain significance ★ ⚠ same residue
DCK p.Ala2Val Uncertain significance ★ ⚠ same type
DCK p.Asn39Ser Uncertain significance ★ ⚠ same type
DCK p.Asn60Ser 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-asp160asn (accessed [today's date]).

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