TATDN2

protein-coding

TatD DNase domain containing 2

Gene summary

Predicted to enable exonuclease activity and metal ion binding activity. Predicted to be located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_014760.4

Inheritance

—

ClinVar variants

U:108B:10

Top phenotype

TATDN2-related disorder

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr3:10,248,023-10,281,218

External References & Databases

Ensembl (ENSG00000157014)

Transcript & Mutation Effects

hg38 • Region Span ~33.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TATDN2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 107

not providedTotal: 2

TATDN2-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014760.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	3 clinvar		7
missense			104 clinvar	7 clinvar		111
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	108	10	0	118

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014760.4	RefSeq	NP_055575.3	6	MANE Select
ENST00000448281.7	Ensembl	ENSP00000408736.2	6	MANE Select
ENST00000287652.8	Ensembl	ENSP00000287652.4	6	Standard
ENST00000287652.9	Ensembl	ENSP00000287652.4	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

XBP1(S) activates chaperone genes

Biological Process

DNA metabolic process
IRE1-mediated unfolded protein response
nucleic acid phosphodiester bond hydrolysis

Molecular Function

endodeoxyribonuclease activity, producing 5'-phosphomonoesters
metal ion binding

Cellular Component

nucleus
nucleoplasm
cytosol
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000287652
Coding exons: 6
Length: 33196
Individuals with no LoFs: 125700
Homozygous LoFs: 0
Heterozygous LoFs: 48
Defined: 125748
p: 0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0537	423	420	1.01	0.0000221	4985
Missense (PolyPhen)		69	98.281	0.70207		1196
Synonymous	-0.653	173	162	1.07	0.00000862	1516
Loss of Function	2.22	15	27.6	0.544	0.00000150	341

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00016	0.00016	rare
Finnish	0.00042	0.00042	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00016	0.00016	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative deoxyribonuclease. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.747
RVIS EVS: 0.67
RVIS percentile EVS: 84.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.344

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium