Is DST p.Tyr1196fs (c.3586dup) pathogenic?

DST p.Tyr1196fs (c.3586dup) is classified Pathogenic/Likely pathogenic in DST (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-04-25). Very rare (popmax 0.00267%, afr); Associated with hereditary sensory and autonomic neuropathy type 6.

What condition is associated with DST p.Tyr1196fs (c.3586dup)?

DST p.Tyr1196fs (c.3586dup) is associated with hereditary sensory and autonomic neuropathy type 6, epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency (ClinVar).

How common is DST p.Tyr1196fs (c.3586dup) in the general population?

DST p.Tyr1196fs (c.3586dup) is very rare (popmax 0.00267%, afr) (gnomAD).

DST p.Tyr1196fs

Q: How is Hereditary sensory and autonomic neuropathy type 6 inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.3586dup · VCV3338558

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Conditions

hereditary sensory and autonomic neuropathy type 6

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 2.9	GERP 1.3, phastCons 1
Overall
CADD	21.3	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 · 2/74,942 alleles

Filtering AF 0.000443% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000166%

Overall 0.00131% 2/152,216 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.Tyr1196fs
Coding: c.3586dup
MANE Select: NM_001374736 · reported on NM_001723
Type: Duplication
Location: chr6:56620447 (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

hereditary sensory and autonomic neuropathy type 6 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency

For Hereditary sensory and autonomic neuropathy type 6 (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

DST p.Thr1727fs Pathogenic ★★ same condition
DST p.Phe1022dup Uncertain significance ★★ same condition
DST p.Ala1361fs Pathogenic ★ same condition
DST p.Arg6274fs Pathogenic ★ same condition
DST p.Asn5081fs Pathogenic ★ same condition
DST p.Gln1818fs Pathogenic ★ same condition
DST p.Glu1516fs Pathogenic ★ same condition
DST p.Glu1834fs 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/dst-p-tyr1196fs (accessed [today's date]).

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