Is DSTYK p.Gln413fs (c.1238del) pathogenic?

DSTYK p.Gln413fs (c.1238del) is classified Uncertain significance in DSTYK (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-11). Absent from gnomAD.

How common is DSTYK p.Gln413fs (c.1238del) in the general population?

DSTYK p.Gln413fs (c.1238del) is absent from gnomAD (gnomAD).

DSTYK p.Gln413fs

c.1238del · rs2102413092 · VCV1376265

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 3 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.12	GERP -1.3, phastCons 0.94

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: DSTYK
Protein: p.Gln413fs
Coding: c.1238del
MANE Select: NM_015375
dbSNP: rs2102413092
Type: Deletion
Location: chr1:205169249 (GRCh38)
Gene constraint: LOEUF 0.445 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 81.02
Residue 413: 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.Asn922fs Uncertain significance ★★ same type
DSTYK p.Arg497del Uncertain significance ★ same type
DSTYK p.Gly661fs Uncertain significance ★ same type
DSTYK c.1949-11_1949-10del Likely benign ★ same type
DSTYK c.2467+245del Benign ★ same type
DSTYK p.Glu297fs Likely pathogenic same type
DSTYK p.Arg46fs 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-gln413fs (accessed [today's date]).

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