Is TH p.Thr245Pro (c.733A>C) pathogenic?

TH p.Thr245Pro (c.733A>C) is classified Uncertain significance in TH (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-27). AlphaMissense: likely benign (0.2013); Very rare (popmax 0.000941%, nfe); Associated with TH-deficient dopa-responsive dystonia.

What condition is associated with TH p.Thr245Pro (c.733A>C)?

TH p.Thr245Pro (c.733A>C) is associated with TH-deficient dopa-responsive dystonia (ClinVar).

How common is TH p.Thr245Pro (c.733A>C) in the general population?

TH p.Thr245Pro (c.733A>C) is very rare (popmax 0.000941%, nfe) (gnomAD).

How is Autosomal recessive dopa-responsive dystonia inherited?

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

What do computational predictors say about TH p.Thr245Pro (c.733A>C)?

AlphaMissense predicts likely benign (score 0.2013) — an in-silico prediction, not a clinical call.

TH p.Thr245Pro

c.733A>C · rs28934581 · VCV12329

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2013 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000941%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

TH-deficient dopa-responsive dystonia

Computational evidence

Protein change
AlphaMissense	0.2013	likely benign
REVEL	0.906	moderately pathogenic-leaning
SaProt	LLR -15.86	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 5.8	GERP 1.8, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 7,550 bp · p 0.38 · regional, not allelic
Overall
CADD	24.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM T276P vs ClinVar T245P) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000941% European (non-Finnish) · 11/1,168,492 alleles

Filtering AF 0.000505% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000369%

Overall 0.000692% 11/1,589,648 alleles · very rare exomes 11/1,437,338 · genomes 0/152,310 · 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: TH
Protein: p.Thr245Pro
Coding: c.733A>C
MANE Select: NM_000360
dbSNP: rs28934581
Type: single nucleotide variant
Location: chr11:2166995 (GRCh38)
Gene constraint: LOEUF 1.27 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.75 · 7 PDB
Residue 276 UniProt numbering: a UniProt-annotated variant site (in arsegs; parkinsonian symptoms in infancy; no effect on tyrosine 3-monooxygenase activity); an α-helix

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

Disease context

TH-deficient dopa-responsive dystonia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal recessive dopa-responsive dystonia (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

TH c.1200+2T>C Likely pathogenic ★★ same condition
TH c.1334+1G>A Likely pathogenic ★★ same condition
TH c.312+1G>A Likely pathogenic ★★ same condition
TH c.488-1G>A Pathogenic ★★ same condition
TH c.644+1G>A Likely pathogenic ★★ same condition
TH c.695+1G>C Likely pathogenic ★★ same condition
TH c.90+10C>T Pathogenic/Likely pathogenic ★★ same condition
TH c.90+13G>A 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/th-p-thr245pro (accessed [today's date]).

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