Is PDYN p.Asp167= (c.501C>T) pathogenic?

PDYN p.Asp167= (c.501C>T) is classified Uncertain significance in PDYN (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Very rare (popmax 8.47e-05%, nfe); Associated with spinocerebellar ataxia type 23.

What condition is associated with PDYN p.Asp167= (c.501C>T)?

PDYN p.Asp167= (c.501C>T) is associated with spinocerebellar ataxia type 23 (ClinVar).

How common is PDYN p.Asp167= (c.501C>T) in the general population?

PDYN p.Asp167= (c.501C>T) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

How is Spinocerebellar ataxia type 23 inherited?

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

PDYN p.Asp167=

c.501C>T · rs886056535 · VCV337837

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

spinocerebellar ataxia type 23

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.87	GERP -5.2, phastCons 0.34
Overall
CADD	5.021	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,034 alleles

Overall 6.2e-05% 1/1,613,968 alleles · very rare exomes 0/1,461,894 · genomes 1/152,074 · joint denominator

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.Asp167=
Coding: c.501C>T
MANE Select: NM_024411
dbSNP: rs886056535
Type: single nucleotide variant
Location: chr20:1980587 (GRCh38)
Gene constraint: LOEUF 0.769 · pLI 0.49 (gnomAD)
Structure: AlphaFold pLDDT 58.95 · 8 PDB

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

Similar variants

PDYN p.Arg180Cys Uncertain significance ★★ ⚠ same condition
PDYN p.Arg231Trp Uncertain significance ★★ ⚠ same condition
PDYN p.Glu242Lys Uncertain significance ★★ ⚠ same condition
PDYN p.Gly191Trp Uncertain significance ★★ ⚠ same condition
PDYN c.*1030C>T Benign ★★ same condition
PDYN c.*356T>C Benign ★★ same condition
PDYN c.*743T>C Benign ★★ same condition
PDYN p.Glu192Val Benign/Likely benign ★★ 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/pdyn-p-asp167 (accessed [today's date]).

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