HTATSF1

HIV-1 Tat specific factor 1, the group of RNA binding motif containing

Basic information

Region (hg38): X:136497079-136512346

Links

ENSG00000102241 ∙ NCBI:27336 ∙ OMIM:300346 ∙ HGNC:5276 ∙ Uniprot:O43719 ∙ 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 HTATSF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTATSF1 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		2
missense			30	3		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	30	5	0

Variants in HTATSF1

This is a list of pathogenic ClinVar variants found in the HTATSF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-136497706-G-A		not specified	Uncertain significance (Jul 02, 2024)
X-136497775-C-G		not specified	Uncertain significance (Feb 07, 2025)
X-136497782-A-T		not specified	Uncertain significance (Nov 08, 2021)
X-136497796-C-G		not specified	Uncertain significance (Jun 27, 2022)
X-136497803-C-T		not specified	Uncertain significance (Jan 01, 2025)
X-136497805-C-T		not specified	Likely benign (Sep 27, 2024)
X-136497856-G-T		not specified	Uncertain significance (Feb 23, 2023)
X-136499613-A-C		not specified	Uncertain significance (Oct 27, 2022)
X-136499619-A-G		not specified	Uncertain significance (Aug 08, 2023)
X-136499638-G-A		not specified	Uncertain significance (Apr 27, 2023)
X-136499673-A-C		not specified	Uncertain significance (Jan 24, 2025)
X-136499739-G-A		not specified	Uncertain significance (Mar 03, 2025)
X-136500689-T-C			Likely benign (Apr 01, 2022)
X-136510171-T-A			Likely benign (Apr 01, 2023)
X-136510832-G-C		not specified	Uncertain significance (Nov 22, 2023)
X-136510943-A-G		not specified	Uncertain significance (Jun 30, 2024)
X-136510947-A-G		not specified	Uncertain significance (Feb 08, 2023)
X-136510956-A-G		not specified	Uncertain significance (Aug 19, 2024)
X-136510971-C-A		not specified	Uncertain significance (Jan 26, 2023)
X-136511024-G-A		not specified	Uncertain significance (Mar 01, 2023)
X-136511088-A-G		not specified	Uncertain significance (Dec 03, 2024)
X-136511097-A-G		not specified	Uncertain significance (Apr 01, 2024)
X-136511108-G-A		not specified	Uncertain significance (Dec 21, 2024)
X-136511211-A-G		not specified	Likely benign (Aug 28, 2023)
X-136511216-G-A		not specified	Uncertain significance (Jan 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTATSF1	protein_coding	protein_coding	ENST00000535601	9	15268

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00260	125650	0	3	125653	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.98	177	268	0.659	0.0000195	5078
Missense in Polyphen		9	48.019	0.18742		939
Synonymous	-0.303	111	107	1.04	0.00000866	1292
Loss of Function	4.14	1	21.9	0.0457	0.00000157	445

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000771	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000247	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a general transcription factor playing a role in the process of transcriptional elongation. May mediate the reciprocal stimulatory effect of splicing on transcriptional elongation. In case of infection by HIV-1, it is up-regulated by the HIV-1 proteins NEF and gp120, acts as a cofactor required for the Tat-enhanced transcription of the virus. {ECO:0000269|PubMed:10393184, ECO:0000269|PubMed:10454543, ECO:0000269|PubMed:10913173, ECO:0000269|PubMed:11420046, ECO:0000269|PubMed:11780068, ECO:0000269|PubMed:15905670, ECO:0000269|PubMed:8849451, ECO:0000269|PubMed:9765201}.

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.395
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.484
• hipred: Y
• hipred_score: 0.662
• ghis: 0.580

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.725

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Htatsf1

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;viral genome replication;regulation of DNA-templated transcription, elongation
• Cellular component: nucleus;nucleoplasm;U2-type spliceosomal complex;U2 snRNP
• Molecular function: RNA binding