Is DST p.Arg593= (c.1779G>A) pathogenic?

DST p.Arg593= (c.1779G>A) is classified Uncertain significance in DST (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-08-31). Ultra-rare (popmax 0.0646%, eas); Associated with Inborn genetic diseases.

How common is DST p.Arg593= (c.1779G>A) in the general population?

DST p.Arg593= (c.1779G>A) is ultra-rare (popmax 0.0646%, eas) (gnomAD).

DST p.Arg593=

Q: What condition is associated with DST p.Arg593= (c.1779G>A)?

DST p.Arg593= (c.1779G>A) is associated with Inborn genetic diseases, hereditary sensory and autonomic neuropathy type 6, epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency (ClinVar).

c.1779G>A · rs759216859 · VCV541470

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0646%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.52 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.1	GERP 1.1, phastCons 1
Overall
CADD	17.61	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0646% East Asian · 29/44,876 alleles

Filtering AF 0.0461% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.04%

Overall 0.00273% 44/1,612,422 alleles · ultra-rare exomes 36/1,460,276 · genomes 8/152,146 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0646%	1,547
Remaining individualsnot grpmax-eligible	0.00481%	20,807
South Asian	0.0033%	30,349
European (non-Finnish)	0.000764%	130,959

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.Arg593=
Coding: c.1779G>A
MANE Select: NM_001374736
dbSNP: rs759216859
Type: single nucleotide variant
Location: chr6:56642503 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary sensory and autonomic neuropathy type 6 epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency

Similar variants

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
DST p.Gln1366Ter 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-arg593 (accessed [today's date]).

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