TARBP1

TAR (HIV-1) RNA binding protein 1, the group of SPOUT methyltransferase domain containing|Armadillo like helical domain containing

Basic information

Region (hg38): 1:234391312-234479179

Links

ENSG00000059588 ∙ NCBI:6894 ∙ OMIM:605052 ∙ HGNC:11568 ∙ Uniprot:Q13395 ∙ 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 TARBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TARBP1 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				2	1	3
missense			112	4	2	118
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	112	6	3

Variants in TARBP1

This is a list of pathogenic ClinVar variants found in the TARBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-234391666-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-234391677-T-C		not specified	Uncertain significance (Oct 20, 2023)
1-234391718-A-T		not specified	Uncertain significance (Apr 22, 2024)
1-234392490-A-C		not specified	Uncertain significance (Dec 01, 2022)
1-234392503-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-234393422-G-C		not specified	Uncertain significance (Nov 08, 2021)
1-234393660-G-A		not specified	Uncertain significance (Jul 14, 2021)
1-234393723-C-T		not specified	Uncertain significance (Jan 03, 2022)
1-234393724-G-C		not specified	Uncertain significance (Jun 17, 2022)
1-234393754-C-T		not specified	Uncertain significance (Jun 07, 2024)
1-234393807-G-A		not specified	Uncertain significance (Jan 22, 2024)
1-234393807-G-C		not specified	Uncertain significance (Oct 12, 2022)
1-234393823-C-T		not specified	Uncertain significance (Jan 03, 2022)
1-234393837-C-T		not specified	Uncertain significance (May 29, 2024)
1-234398396-G-C		not specified	Uncertain significance (Apr 26, 2023)
1-234398418-T-C		not specified	Likely benign (Mar 16, 2022)
1-234398531-C-T		not specified	Uncertain significance (Mar 14, 2023)
1-234398552-G-C		not specified	Uncertain significance (Dec 22, 2023)
1-234401201-G-A		not specified	Uncertain significance (Jan 08, 2024)
1-234401205-G-C		not specified	Uncertain significance (Nov 01, 2022)
1-234401239-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-234405907-C-T		not specified	Uncertain significance (Nov 29, 2021)
1-234405966-A-C		not specified	Uncertain significance (May 24, 2023)
1-234405994-C-T		not specified	Likely benign (Nov 22, 2021)
1-234405996-G-C		not specified	Likely benign (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TARBP1	protein_coding	protein_coding	ENST00000040877	30	87791

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.39e-23	0.946	125573	1	174	125748	0.000696

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.429	758	726	1.04	0.0000358	10415
Missense in Polyphen		216	243.1	0.88851		3580
Synonymous	0.881	254	273	0.932	0.0000139	3198
Loss of Function	2.68	48	72.6	0.661	0.00000335	960

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00238	0.00227
Ashkenazi Jewish	0.000410	0.000397
East Asian	0.00105	0.000979
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000760	0.000739
Middle Eastern	0.00105	0.000979
South Asian	0.000652	0.000588
Other	0.000496	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable S-adenosyl-L-methionine-dependent methyltransferase which methylates RNA molecules such as tRNAs. In case of infection by HIV-1, it binds to the loop region of TAR RNA, a region also bound by RNA polymerase II. Binding of TARBP1 and RNA polymerase II to HIV-1 TAR RNA is mutually exclusive, suggesting that TARBP1 may function alone or in conjunction with HIV-1 Tat to disengage RNA polymerase II from HIV-1 TAR RNA. May act by methylating HIV-1 TAR RNA. {ECO:0000269|PubMed:7638159, ECO:0000269|PubMed:8626763, ECO:0000269|PubMed:8846792}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.993
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.36

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.377
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.557

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tarbp1

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;tRNA methylation
• Cellular component: nucleus
• Molecular function: RNA binding;tRNA (guanine) methyltransferase activity