Is DST p.Val7686= (c.23058G>A) pathogenic?

DST p.Val7686= (c.23058G>A) is classified Benign/Likely benign in DST (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-03). Low-frequency (popmax 4.53%, nfe); Associated with epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency.

How common is DST p.Val7686= (c.23058G>A) in the general population?

DST p.Val7686= (c.23058G>A) is low-frequency (popmax 4.53%, nfe) (gnomAD).

DST p.Val7686=

Q: What condition is associated with DST p.Val7686= (c.23058G>A)?

DST p.Val7686= (c.23058G>A) is associated with epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency, hereditary sensory and autonomic neuropathy type 6 (ClinVar).

Q: How is Epidermolysis bullosa simplex due to BP230 deficiency inherited?

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

c.23058G>A · rs144012429 · VCV1164482

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

low-frequency (popmax 4.53%, nfe)

Conditions

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

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 1.4	GERP 2.1, phastCons 1
Overall
CADD	5.292	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.53% European (non-Finnish) · 53,205/1,175,458 alleles

Filtering AF 4.49% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.48%

Overall 3.76% 60,501/1,607,908 alleles · low-frequency exomes 56,695/1,455,682 · genomes 3,806/152,226 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	4.53%	22
Ashkenazi Jewishnot grpmax-eligible	4.52%	22
Remaining individualsnot grpmax-eligible	3.52%	28
South Asian	1.67%	60
Admixed American	1.38%	72
Finnishnot grpmax-eligible	1.31%	76
African / African-American	0.746%	134
Middle Eastern	0.513%	195
East Asian	0.0112%	8,967

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.Val7686=
Coding: c.23058G>A
MANE Select: NM_001374736
dbSNP: rs144012429
Type: single nucleotide variant
Location: chr6:56463058 (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

epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary sensory and autonomic neuropathy type 6

For Epidermolysis bullosa simplex due to BP230 deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Adult

Similar variants

DST p.Val7686Met Uncertain significance ★ same residue
DST c.22959+1G>A Likely pathogenic ★★ same condition
DST p.Arg1512Ter Pathogenic/Likely pathogenic ★★ same condition
DST p.Arg1696Ter Pathogenic/Likely pathogenic ★★ same condition
DST p.Arg22Ter Likely pathogenic ★★ same condition
DST p.Arg7329Ter Pathogenic ★★ same condition
DST p.Cys1828Ter Pathogenic/Likely pathogenic ★★ same condition
DST p.Gln1124Ter 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-val7686 (accessed [today's date]).

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