Is DSTYK p.Trp8Ter (c.24G>A) pathogenic?

DSTYK p.Trp8Ter (c.24G>A) is classified Pathogenic in DSTYK (ClinVar, No assertion criteria, 1 submitter; last evaluated 2013-08-15). Absent from gnomAD v4.1; Associated with congenital anomalies of kidney and urinary tract 1.

What condition is associated with DSTYK p.Trp8Ter (c.24G>A)?

DSTYK p.Trp8Ter (c.24G>A) is associated with congenital anomalies of kidney and urinary tract 1 (ClinVar).

How common is DSTYK p.Trp8Ter (c.24G>A) in the general population?

DSTYK p.Trp8Ter (c.24G>A) is absent from gnomAD v4.1 (gnomAD).

DSTYK p.Trp8Ter

c.24G>A · rs879255515 · VCV60685

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,560,058)

Conditions

congenital anomalies of kidney and urinary tract 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 1 of 13
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.8	GERP 1.5, phastCons 1
Overall
CADD	35.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,560,058). 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.Trp8Ter
Coding: c.24G>A
MANE Select: NM_015375
dbSNP: rs879255515
Type: single nucleotide variant
Location: chr1:205211512 (GRCh38)
Gene constraint: LOEUF 0.445 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 81.02
Residue 8: a UniProt-annotated variant site (in cakut1; uncertain significance); the 'disordered' region

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

Disease context

congenital anomalies of kidney and urinary tract 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DSTYK p.Trp8Gly Uncertain significance ★★ ⚠ same residue
DSTYK p.Trp8Arg Uncertain significance ★ ⚠ same residue
DSTYK p.Trp8Leu Uncertain significance ★ ⚠ same residue
DSTYK p.Arg626Gln Uncertain significance ★★ ⚠ same condition
DSTYK p.Gly32Asp Uncertain significance ★★ ⚠ same condition
DSTYK p.Cys641Arg Benign ★★ same condition
DSTYK p.Phe676= Benign ★★ same condition
DSTYK p.Gln465Arg Likely pathogenic ★ 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/dstyk-p-trp8ter (accessed [today's date]).

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