Is DST p.Asn3099fs (c.9296_9299del) pathogenic?

DST p.Asn3099fs (c.92969299del) is classified Pathogenic in DST (ClinVar, No assertion criteria, 1 submitter; last evaluated 2026-03-05). Very rare (popmax 0.00267%, afr); Associated with congenital myopathy 29 with contractures.

What condition is associated with DST p.Asn3099fs (c.9296_9299del)?

DST p.Asn3099fs (c.9296_9299del) is associated with congenital myopathy 29 with contractures (ClinVar).

How common is DST p.Asn3099fs (c.9296_9299del) in the general population?

DST p.Asn3099fs (c.9296_9299del) is very rare (popmax 0.00267%, afr) (gnomAD).

DST p.Asn3099fs

c.9296_9299del · VCV4813117

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Conditions

congenital myopathy 29 with contractures

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 40 of 104
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.4	GERP -5.6
Overall
CADD	22.9	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 0.00267% African / African-American · 2/74,814 alleles

Filtering AF 0.000444% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000166%

Overall 0.000186% 3/1,612,136 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,407
Remaining individualsnot grpmax-eligible	0.0016%	62,352

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.Asn3099fs
Coding: c.9296_9299del
MANE Select: NM_001374736
Type: Microsatellite
Location: chr6:56605329 (GRCh38)
Gene constraint: LOEUF 0.297 · pLI 1.00 (gnomAD)

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

Disease context

congenital myopathy 29 with contractures — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DST p.Pro1950_Val1951insTer Pathogenic ★ same condition
DST p.Gln3326Ter Pathogenic same condition
DST p.Leu3636fs Pathogenic same condition
DST p.Tyr2613Ter Pathogenic same condition
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

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-asn3099fs (accessed [today's date]).

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