Is PDYN p.Asp194= (c.582C>T) pathogenic?

PDYN p.Asp194= (c.582C>T) is classified Conflicting classifications of pathogenicity in PDYN (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2024-05-03). Ultra-rare (popmax 0.0121%, afr); Associated with spinocerebellar ataxia type 23.

What condition is associated with PDYN p.Asp194= (c.582C>T)?

PDYN p.Asp194= (c.582C>T) is associated with spinocerebellar ataxia type 23 (ClinVar).

How common is PDYN p.Asp194= (c.582C>T) in the general population?

PDYN p.Asp194= (c.582C>T) is ultra-rare (popmax 0.0121%, afr) (gnomAD).

How is Spinocerebellar ataxia type 23 inherited?

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

PDYN p.Asp194=

c.582C>T · rs769461186 · VCV728105

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0121%, afr)

Conditions

spinocerebellar ataxia type 23

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -9.9	GERP -3.4
Overall
CADD	0.02	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0121% African / African-American · 9/74,622 alleles

Filtering AF 0.00758% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00706%

Overall 0.00738% 119/1,612,356 alleles · ultra-rare exomes 109/1,460,828 · genomes 10/151,528 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0121%	8,291
European (non-Finnish)	0.00899%	11,124
Remaining individualsnot grpmax-eligible	0.00641%	15,603

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: PDYN
Protein: p.Asp194=
Coding: c.582C>T
MANE Select: NM_024411
dbSNP: rs769461186
Type: single nucleotide variant
Location: chr20:1980506 (GRCh38)

Full PDYN gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

spinocerebellar ataxia type 23 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Spinocerebellar ataxia type 23 (Orphanet):

Inheritance: Autosomal dominant
Onset: Adult

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/pdyn-p-asp194 (accessed [today's date]).

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