Is DSTYK p.Ala817= (c.2451C>A) pathogenic?

DSTYK p.Ala817= (c.2451C>A) is classified Likely benign in DSTYK (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-09). Absent from gnomAD v4.1.

How common is DSTYK p.Ala817= (c.2451C>A) in the general population?

DSTYK p.Ala817= (c.2451C>A) is absent from gnomAD v4.1 (gnomAD).

DSTYK p.Ala817=

c.2451C>A · VCV4724707

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.5	GERP 2.3, phastCons 1
Overall
CADD	9.274	PHRED · no single calibrated threshold — expert panels disagree

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: DSTYK
Protein: p.Ala817=
Coding: c.2451C>A
MANE Select: NM_015375
Type: single nucleotide variant
Location: chr1:205150696 (GRCh38)
Gene constraint: LOEUF 0.445 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 81.02
Residue 817: the protein kinase domain; a UniProt-annotated variant site (in cakut1; uncertain significance)

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

Similar variants

DSTYK p.Ala817Gly Uncertain significance ★ ⚠ same residue
DSTYK p.Ala817Thr Uncertain significance ★ same residue
DSTYK p.Ala206Val Uncertain significance ★★ ⚠ same type
DSTYK p.Ala477Ser Uncertain significance ★★ ⚠ same type
DSTYK p.Ala601Val Uncertain significance ★★ ⚠ same type
DSTYK p.Arg411Gln Uncertain significance ★★ ⚠ same type
DSTYK p.Arg462Gln Uncertain significance ★★ ⚠ same type
DSTYK p.Arg471Gln 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/dstyk-p-ala817 (accessed [today's date]).

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