Is DST p.Gln2515Ter (c.7543C>T) pathogenic?

DST p.Gln2515Ter (c.7543C>T) is classified Pathogenic in DST (ClinVar, Single submitter, 1 submitter; last evaluated 2016-12-13). Very rare (popmax 0.00223%, eas).

How common is DST p.Gln2515Ter (c.7543C>T) in the general population?

DST p.Gln2515Ter (c.7543C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

DST p.Gln2515Ter

c.7543C>T · rs1057524203 · VCV391713

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

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-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.9	GERP 2.8, phastCons 1
Overall
CADD	23.1	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 0.00223% East Asian · 1/44,882 alleles

Overall 6.84e-05% 1/1,461,874 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.Gln2515Ter
Coding: c.7543C>T
MANE Select: NM_001374736 · reported on NM_001723
dbSNP: rs1057524203
Type: single nucleotide variant
Location: chr6:56615924 (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 c.22959+1G>A Likely pathogenic ★★ same type
DST p.Arg1512Ter Pathogenic/Likely pathogenic ★★ same type
DST p.Arg1696Ter Pathogenic/Likely pathogenic ★★ same type
DST p.Arg22Ter Likely pathogenic ★★ same type
DST p.Arg7329Ter Pathogenic ★★ same type
DST p.Cys1828Ter Pathogenic/Likely pathogenic ★★ same type
DST p.Gln1124Ter Pathogenic/Likely pathogenic ★★ same type
DST p.Gln1366Ter Pathogenic/Likely pathogenic ★★ 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-gln2515ter (accessed [today's date]).

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