Is DACT1 p.Thr736Ile (c.2207C>T) pathogenic?

DACT1 p.Thr736Ile (c.2207C>T) is classified Uncertain significance in DACT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-01-01). AlphaMissense: likely pathogenic (0.5841); Very rare (popmax 0.000339%, nfe); Associated with Townes-Brocks syndrome 2.

What condition is associated with DACT1 p.Thr736Ile (c.2207C>T)?

DACT1 p.Thr736Ile (c.2207C>T) is associated with Townes-Brocks syndrome 2 (ClinVar).

How common is DACT1 p.Thr736Ile (c.2207C>T) in the general population?

DACT1 p.Thr736Ile (c.2207C>T) is very rare (popmax 0.000339%, nfe) (gnomAD).

What do computational predictors say about DACT1 p.Thr736Ile (c.2207C>T)?

AlphaMissense predicts likely pathogenic (score 0.5841) — an in-silico prediction, not a clinical call.

DACT1 p.Thr736Ile

c.2207C>T · rs2047696489 · VCV982996

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.5841 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000339%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Townes-Brocks syndrome 2

Computational evidence

Protein change
AlphaMissense	0.5841	likely pathogenic
REVEL	0.074	moderately benign-leaning
SaProt	LLR -8.03	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.3	GERP 0.51, phastCons 1
Regional constraint	o/e 1.10	unconstrained · MANE · 8,733 bp · p 0.0021 · regional, not allelic
Overall
CADD	23.2	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 T773I vs ClinVar T736I) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000339% European (non-Finnish) · 4/1,180,050 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000248% 4/1,614,090 alleles · very rare

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: DACT1
Protein: p.Thr736Ile
Coding: c.2207C>T
MANE Select: NM_001079520
dbSNP: rs2047696489
Type: single nucleotide variant
Location: chr14:58646941 (GRCh38)
Gene constraint: LOEUF 0.703 · pLI 0.17 (gnomAD)
Structure: AlphaFold pLDDT 50.95
Residue 736: a UniProt-annotated variant site (in tbs2; the mutant protein is stable and expressed)

Full DACT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Townes-Brocks syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DACT1 p.Glu451Asp Uncertain significance ★★ ⚠ same condition
DACT1 p.Ala427Val Benign ★★ same condition
DACT1 p.Glu257Lys Benign/Likely benign ★★ same condition
DACT1 p.Leu90= Benign ★★ same condition
DACT1 p.Gln310His Conflicting classifications of pathogenicity ★ ⚠ same condition
DACT1 p.Glu708Lys Uncertain significance ★ ⚠ same condition
DACT1 p.Gly744Ser Uncertain significance ★ ⚠ same condition
DACT1 p.Phe376Leu Uncertain significance ★ ⚠ 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/dact1-p-thr736ile (accessed [today's date]).

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