Is DST p.Ser803del (c.2405CTT[1]) pathogenic?

DST p.Ser803del (c.2405CTT[1]) is classified Uncertain significance in DST (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-18). Ultra-rare (popmax 0.0165%, mid); Associated with hereditary sensory and autonomic neuropathy type 6.

What condition is associated with DST p.Ser803del (c.2405CTT[1])?

DST p.Ser803del (c.2405CTT[1]) 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.Ser803del (c.2405CTT[1]) in the general population?

DST p.Ser803del (c.2405CTT[1]) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

DST p.Ser803del

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.2405CTT[1] · rs749412641 · VCV1414977

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

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.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.4, phastCons 1
Overall
CADD	18.47	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,062 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.000434% 7/1,614,204 alleles · ultra-rare exomes 6/1,461,854 · genomes 1/152,350 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,062
South Asian	0.0011%	91,090
European (non-Finnish)	0.000424%	236,007

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.Ser803del
Coding: c.2405CTT[1]
MANE Select: NM_001374736
dbSNP: rs749412641
Type: Microsatellite
Location: chr6:56640223 (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.Phe3921del Uncertain significance ★★ same condition
DST c.21403-23TG[17] Likely benign ★★ same condition
DST c.21403-23TG[18] Benign/Likely benign ★★ same condition
DST c.21403-23TG[19] Benign/Likely benign ★★ same condition
DST c.21403-23TG[20] Likely benign ★★ same condition
DST c.21403-23TG[6] Benign/Likely benign ★★ same condition
DST c.21403-23TG[8] Likely benign ★★ same condition
DST p.Leu1732fs 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-ser803del (accessed [today's date]).

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