Is TH p.Thr463= (c.1389G>A) pathogenic?

TH p.Thr463= (c.1389G>A) is classified Likely benign in TH (ClinVar, Single submitter, 3 submitters; last evaluated 2026-01-21). Very rare (popmax 0.00976%, afr); Associated with TH-deficient dopa-responsive dystonia.

What condition is associated with TH p.Thr463= (c.1389G>A)?

TH p.Thr463= (c.1389G>A) is associated with TH-deficient dopa-responsive dystonia (ClinVar).

How common is TH p.Thr463= (c.1389G>A) in the general population?

TH p.Thr463= (c.1389G>A) is very rare (popmax 0.00976%, afr) (gnomAD).

How is Autosomal recessive dopa-responsive dystonia inherited?

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

TH p.Thr463=

c.1389G>A · rs370029424 · VCV699902

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00976%, afr)

Conditions

TH-deficient dopa-responsive dystonia

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 -14	GERP -3.4
Overall
CADD	0.5	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00976% African / African-American · 7/71,714 alleles

Filtering AF 0.00455% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0032%

Overall 0.00396% 61/1,541,836 alleles · very rare exomes 50/1,389,656 · genomes 11/152,180 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00976%	10,245
Remaining individualsnot grpmax-eligible	0.00675%	14,823
Admixed American	0.00581%	17,225
European (non-Finnish)	0.00403%	24,805
East Asian	0.00241%	41,420

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.Thr463=
Coding: c.1389G>A
MANE Select: NM_000360
dbSNP: rs370029424
Type: single nucleotide variant
Location: chr11:2164338 (GRCh38)
Gene constraint: LOEUF 1.27 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.75 · 7 PDB
Residue 463: a β-strand

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.Thr463Met Conflicting classifications of pathogenicity ★ ⚠ 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
TH c.90+10C>T 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/th-p-thr463 (accessed [today's date]).

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