Is DST p.Lys2630fs (c.7887_7891delinsGTA) pathogenic?

DST p.Lys2630fs (c.78877891delinsGTA) is classified Conflicting classifications of pathogenicity in DST (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-12-10). Absent from gnomAD; Associated with hereditary sensory and autonomic neuropathy type 6.

What condition is associated with DST p.Lys2630fs (c.7887_7891delinsGTA)?

DST p.Lys2630fs (c.7887_7891delinsGTA) 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.Lys2630fs (c.7887_7891delinsGTA) in the general population?

DST p.Lys2630fs (c.7887_7891delinsGTA) is absent from gnomAD (gnomAD).

DST p.Lys2630fs

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.7887_7891delinsGTA · rs1554497505 · VCV541456

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 8.7	GERP 2.6, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: DST
Protein: p.Lys2630fs
Coding: c.7887_7891delinsGTA
MANE Select: NM_001374736 · reported on NM_001723
dbSNP: rs1554497505
Type: Indel
Location: chr6:56615576 (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.Ala4419Leu Uncertain significance ★★ same condition
DST p.Ala5119Leu Uncertain significance ★ same condition
DST p.Gln1393_Leu1394delinsHisPhe Uncertain significance ★ same condition
DST p.Ser7080Lys Uncertain significance ★ same condition
DST p.Ser7810Pro Uncertain significance ★ same condition
DST c.12903+10_12903+11delinsTT Likely benign ★ same condition
DST c.22959+1G>A Likely pathogenic ★★ same condition
DST p.Ala1128fs 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-lys2630fs (accessed [today's date]).

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