Is DST p.Tyr2302fs (c.6901_6902dup) pathogenic?

DST p.Tyr2302fs (c.69016902dup) is classified Likely pathogenic in DST (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-28). Very rare (popmax 0.00667%, afr).

How common is DST p.Tyr2302fs (c.6901_6902dup) in the general population?

DST p.Tyr2302fs (c.6901_6902dup) is very rare (popmax 0.00667%, afr) (gnomAD).

DST p.Tyr2302fs

c.6901_6902dup · VCV4082418

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00667%, afr)

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-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.2	GERP -2.7, phastCons 0.24
Overall
CADD	20.6	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

Grpmax group 0.00667% African / African-American · 5/74,908 alleles

Filtering AF 0.00255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00161%

Overall 0.00031% 5/1,614,024 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DST
Protein: p.Tyr2302fs
Coding: c.6901_6902dup
MANE Select: NM_001374736 · reported on NM_001723
Type: Microsatellite
Location: chr6:56616564 (GRCh38)
Gene constraint: LOEUF 0.297 · pLI 1.00 (gnomAD)

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

Similar variants

DST p.Tyr2302Cys Uncertain significance ★ same residue
DST p.Tyr2302Ter Uncertain significance ★ same residue
DST p.Phe3921del Uncertain significance ★★ same type
DST c.21403-23TG[17] Likely benign ★★ same type
DST c.21403-23TG[18] Benign/Likely benign ★★ same type
DST c.21403-23TG[19] Benign/Likely benign ★★ same type
DST c.21403-23TG[20] Likely benign ★★ same type
DST c.21403-23TG[6] Benign/Likely benign ★★ 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/dst-p-tyr2302fs (accessed [today's date]).

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