Is DST p.Ile4903= (c.14709T>A) pathogenic?

DST p.Ile4903= (c.14709T>A) is classified Likely benign in DST (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-04-27). Rare (popmax 0.27%, mid); Associated with hereditary sensory and autonomic neuropathy type 6.

What condition is associated with DST p.Ile4903= (c.14709T>A)?

DST p.Ile4903= (c.14709T>A) 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.Ile4903= (c.14709T>A) in the general population?

DST p.Ile4903= (c.14709T>A) is rare (popmax 0.27%, mid) (gnomAD).

DST p.Ile4903=

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.14709T>A · rs199986238 · VCV1093781

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.27%, 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 · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.14	GERP -0.66, phastCons 0.15
Overall
CADD	3.881	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.27% Middle Eastern · 16/5,932 alleles

Filtering AF 0.169% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.138%

Overall 0.00808% 128/1,584,208 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.27%	371
Remaining individualsnot grpmax-eligible	0.0131%	7,631
Admixed American	0.00853%	11,729
European (non-Finnish)	0.00802%	12,474
Ashkenazi Jewishnot grpmax-eligible	0.00706%	14,170
South Asian	0.00343%	29,129
African / African-American	0.00134%	74,394

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.Ile4903=
Coding: c.14709T>A
MANE Select: NM_001374736
dbSNP: rs199986238
Type: single nucleotide variant
Location: chr6:56555772 (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

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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-ile4903 (accessed [today's date]).

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