TATDN1

TatD DNase domain containing 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 8:124488484-124539458

Links

ENSG00000147687 ∙ NCBI:83940 ∙ OMIM:619364 ∙ HGNC:24220 ∙ Uniprot:Q6P1N9 ∙ 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 TATDN1 gene.

• Inborn genetic diseases (16 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TATDN1 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						0
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	16	1	0

Variants in TATDN1

This is a list of pathogenic ClinVar variants found in the TATDN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-124488602-C-T		not specified	Uncertain significance (Aug 04, 2023)
8-124488610-A-G		not specified	Uncertain significance (Dec 01, 2022)
8-124488661-T-C		not specified	Uncertain significance (Sep 29, 2022)
8-124488684-C-G		not specified	Uncertain significance (Jan 03, 2024)
8-124493851-T-A		not specified	Uncertain significance (Apr 12, 2023)
8-124493878-T-C		not specified	Uncertain significance (Jul 06, 2021)
8-124493879-C-G		not specified	Uncertain significance (Oct 29, 2021)
8-124493927-C-T		not specified	Uncertain significance (Oct 12, 2021)
8-124493953-G-T		not specified	Uncertain significance (Dec 19, 2023)
8-124495495-C-G		not specified	Uncertain significance (Jan 04, 2024)
8-124504322-T-C		not specified	Uncertain significance (May 08, 2023)
8-124508494-C-T		not specified	Uncertain significance (Feb 06, 2023)
8-124515779-C-T		not specified	Uncertain significance (Dec 20, 2023)
8-124515904-A-G		not specified	Uncertain significance (Mar 14, 2023)
8-124515920-C-T		not specified	Uncertain significance (Dec 30, 2023)
8-124515934-G-C		not specified	Uncertain significance (Dec 03, 2021)
8-124515938-G-T		not specified	Uncertain significance (Jan 05, 2022)
8-124515962-G-A		not specified	Uncertain significance (Jun 07, 2023)
8-124515968-G-A		not specified	Uncertain significance (Sep 29, 2023)
8-124518820-T-C		not specified	Uncertain significance (Oct 13, 2023)
8-124522952-C-A		not specified	Uncertain significance (Apr 25, 2023)
8-124522975-A-G		not specified	Uncertain significance (Mar 01, 2024)
8-124522999-A-G		not specified	Uncertain significance (Feb 21, 2024)
8-124523000-T-C		not specified	Uncertain significance (Mar 08, 2024)
8-124539034-T-G		not specified	Uncertain significance (May 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TATDN1	protein_coding	protein_coding	ENST00000276692	12	50974

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.49e-16	0.00407	125667	0	81	125748	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.181	155	149	1.04	0.00000676	1967
Missense in Polyphen		56	52.821	1.0602		678
Synonymous	0.914	38	45.9	0.828	0.00000204	505
Loss of Function	-0.465	22	19.8	1.11	9.75e-7	259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00100	0.000995
Ashkenazi Jewish	0.00	0.00
East Asian	0.000878	0.000870
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.000312	0.000308
Middle Eastern	0.000878	0.000870
South Asian	0.0000328	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.238
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• pHI: 0.291
• hipred: N
• hipred_score: 0.292
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.158

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tatdn1

Zebrafish Information Network

• Gene name: tatdn1
• Affected structure: eye
• Phenotype tag: abnormal
• Phenotype quality: apoptotic

Gene ontology

• Biological process: DNA metabolic process;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleoplasm
• Molecular function: protein binding;3'-5'-exodeoxyribonuclease activity;endodeoxyribonuclease activity, producing 5'-phosphomonoesters;metal ion binding