Is DST p.Arg1125= (c.3375T>C) pathogenic?

DST p.Arg1125= (c.3375T>C) is classified Likely benign in DST (ClinVar, Single submitter, 1 submitter; last evaluated 2019-09-28). Absent from gnomAD v4.1; Associated with hereditary sensory and autonomic neuropathy type 6.

What condition is associated with DST p.Arg1125= (c.3375T>C)?

DST p.Arg1125= (c.3375T>C) 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.Arg1125= (c.3375T>C) in the general population?

DST p.Arg1125= (c.3375T>C) is absent from gnomAD v4.1 (gnomAD).

DST p.Arg1125=

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.3375T>C · rs2152740248 · VCV1131253

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.007	GERP -4.6, phastCons 0.11
Overall
CADD	9.425	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DST
Protein: p.Arg1125=
Coding: c.3375T>C
MANE Select: NM_001374736 · reported on NM_001723
dbSNP: rs2152740248
Type: single nucleotide variant
Location: chr6:56620659 (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.Ala1125Val Uncertain significance ★★ same residue
DST p.Ala1125= Likely benign ★★ same residue
DST p.Arg1125Cys Uncertain significance ★ same residue
DST p.Arg1125His Uncertain significance ★ same residue
DST p.Arg1125Leu Uncertain significance ★ same residue
DST p.Arg1125Pro Uncertain significance ★ same residue
DST c.22959+1G>A Likely pathogenic ★★ same condition
DST p.Arg1512Ter Pathogenic/Likely 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-arg1125 (accessed [today's date]).

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