Is DACT1 p.Asn336= (c.1008C>T) pathogenic?

DACT1 p.Asn336= (c.1008C>T) is classified Likely benign in DACT1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-27). Rare (popmax 0.128%, afr); Associated with DACT1-related disorder.

What condition is associated with DACT1 p.Asn336= (c.1008C>T)?

DACT1 p.Asn336= (c.1008C>T) is associated with DACT1-related disorder (ClinVar).

How common is DACT1 p.Asn336= (c.1008C>T) in the general population?

DACT1 p.Asn336= (c.1008C>T) is rare (popmax 0.128%, afr) (gnomAD).

DACT1 p.Asn336=

c.1008C>T · rs144700196 · VCV3042774

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.128%, afr)

Conditions

DACT1-related disorder

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 -9.8	GERP -4.4
Overall
CADD	5.34	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.128% African / African-American · 96/74,946 alleles

Filtering AF 0.107% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0997%

Overall 0.00867% 140/1,614,068 alleles · rare exomes 82/1,461,826 · genomes 58/152,242 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.128%	781
South Asian	0.0417%	2,397
Remaining individualsnot grpmax-eligible	0.0032%	31,243
Admixed American	0.00167%	60,018
European (non-Finnish)	0.000254%	393,329

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.Asn336=
Coding: c.1008C>T
MANE Select: NM_001079520
dbSNP: rs144700196
Type: single nucleotide variant
Location: chr14:58645742 (GRCh38)
Gene constraint: LOEUF 0.703 · pLI 0.17 (gnomAD)
Structure: AlphaFold pLDDT 50.95

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

Disease context

DACT1-related disorder

Similar variants

DACT1 p.Ala9Pro Uncertain significance ★ ⚠ same condition
DACT1 p.His426Arg Uncertain significance ★ ⚠ same condition
DACT1 p.Pro295Ala Uncertain significance ★ ⚠ same condition
DACT1 p.Ala677Ser Uncertain significance ⚠ same condition
DACT1 p.Arg85Ser Uncertain significance ⚠ same condition
DACT1 p.Gly560Cys Uncertain significance ⚠ same condition
DACT1 p.Arg659= Likely benign same condition
DACT1 p.Cys207= 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/dact1-p-asn336 (accessed [today's date]).

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