Is TH p.Pro461Arg (c.1382C>G) pathogenic?

TH p.Pro461Arg (c.1382C>G) is classified Uncertain significance in TH (ClinVar, No assertion criteria, 1 submitter; last evaluated 2018-04-10). AlphaMissense: ambiguous (0.4041); No allele count reported in gnomAD v4.1 (AN 1,546,418); Associated with TH-deficient dopa-responsive dystonia.

What condition is associated with TH p.Pro461Arg (c.1382C>G)?

TH p.Pro461Arg (c.1382C>G) is associated with TH-deficient dopa-responsive dystonia (ClinVar).

How common is TH p.Pro461Arg (c.1382C>G) in the general population?

TH p.Pro461Arg (c.1382C>G) is no allele count reported in gnomAD v4.1 (AN 1,546,418) (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.Pro461Arg (c.1382C>G)?

AlphaMissense predicts ambiguous (score 0.4041) — an in-silico prediction, not a clinical call.

TH p.Pro461Arg

c.1382C>G · rs767635052 · VCV557668

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4041 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,546,418)

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Conditions

TH-deficient dopa-responsive dystonia

Computational evidence

Protein change
AlphaMissense	0.4041	ambiguous
REVEL	0.917	moderately pathogenic-leaning
SaProt	LLR -11.66	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 11	GERP 1.7, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 7,550 bp · p 0.38 · regional, not allelic
Overall
CADD	26.0	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 P492R vs ClinVar P461R) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,546,418). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: TH
Protein: p.Pro461Arg
Coding: c.1382C>G
MANE Select: NM_000360
dbSNP: rs767635052
Type: single nucleotide variant
Location: chr11:2164345 (GRCh38)
Gene constraint: LOEUF 1.27 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.75 · 7 PDB
Residue 492 UniProt numbering: a UniProt-annotated variant site (in arsegs; complete loss of tyrosine 3-monooxygenase activity); a turn

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 p.Pro461Leu Pathogenic/Likely pathogenic ★★ same residue
TH p.Pro461= Likely benign ★ same residue
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

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-pro461arg (accessed [today's date]).

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