TATDN2

TatD DNase domain containing 2

Basic information

Region (hg38): 3:10248022-10281218

Links

ENSG00000157014 ∙ NCBI:9797 ∙ OMIM:619330 ∙ HGNC:28988 ∙ Uniprot:Q93075 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TATDN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TATDN2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			29	4		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	7	0

Variants in TATDN2

This is a list of pathogenic ClinVar variants found in the TATDN2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-10249271-G-C		not specified	Uncertain significance (Feb 05, 2024)
3-10249300-C-T		not specified	Uncertain significance (Oct 26, 2022)
3-10249345-C-T		not specified	Uncertain significance (Mar 25, 2024)
3-10249369-G-A		not specified	Uncertain significance (Apr 07, 2022)
3-10249378-G-A		not specified	Uncertain significance (Apr 22, 2024)
3-10249397-C-T		not specified	Uncertain significance (May 14, 2024)
3-10249399-C-T		not specified	Uncertain significance (Jul 26, 2022)
3-10249426-C-T		not specified	Uncertain significance (Dec 13, 2022)
3-10249472-C-G		not specified	Uncertain significance (Jan 04, 2022)
3-10249487-C-T		not specified	Uncertain significance (Dec 28, 2022)
3-10249587-T-G		TATDN2-related disorder	Likely benign (Nov 05, 2020)
3-10260149-G-A		not specified	Uncertain significance (Nov 20, 2023)
3-10260152-A-G		not specified	Uncertain significance (Apr 05, 2023)
3-10260315-C-T		not specified	Uncertain significance (Feb 10, 2022)
3-10260398-A-G		not specified	Uncertain significance (Mar 31, 2022)
3-10260506-A-G		not specified	Uncertain significance (Apr 19, 2023)
3-10260534-A-G		not specified	Likely benign (Sep 29, 2023)
3-10260654-A-G		not specified	Uncertain significance (Mar 01, 2024)
3-10270216-C-G		not specified	Uncertain significance (Apr 07, 2022)
3-10270296-C-G		not specified	Likely benign (Jan 17, 2024)
3-10270356-C-T		not specified	Uncertain significance (May 18, 2022)
3-10270368-C-T		not specified	Uncertain significance (Aug 19, 2023)
3-10270375-C-T		not specified	Uncertain significance (Jan 13, 2023)
3-10270391-C-T			Likely benign (Mar 01, 2022)
3-10270437-T-C		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TATDN2	protein_coding	protein_coding	ENST00000287652	6	33196

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.01e-7	0.984	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0537	423	420	1.01	0.0000221	4985
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000341	0.000335
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000163	0.000163
Finnish	0.000416	0.000416
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.000163	0.000163
South Asian	0.000164	0.000163
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative deoxyribonuclease. {ECO:0000250}.
• Pathway: XBP1(S) activates chaperone genes (Consensus)

Intolerance Scores

• loftool: 0.747
• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.68

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.132
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.344

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tatdn2

Gene ontology

• Biological process: DNA metabolic process;IRE1-mediated unfolded protein response;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleus;nucleoplasm;cytosol;nuclear speck
• Molecular function: endodeoxyribonuclease activity, producing 5'-phosphomonoesters;metal ion binding