HTATSF1

protein-coding

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

Gene summary

The protein encoded by this gene functions as a cofactor for the stimulation of transcriptional elongation by HIV-1 Tat, which binds to the HIV-1 promoter through Tat-TAR interaction. This protein may also serve as a dual-function factor to couple transcription and splicing and to facilitate their reciprocal activation. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Sep 2009]

MANE transcript

NM_014500.5

Inheritance

—

ClinVar variants

U:126B:5

Top phenotype

HTATSF1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chrX:136,497,079-136,512,346

External References & Databases

Ensembl (ENSG00000102241)

Transcript & Mutation Effects

hg38 • Region Span ~15.3 kb

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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 HTATSF1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 2

HTATSF1-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014500.5. 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			5 clinvar	2 clinvar		7
missense			100 clinvar	3 clinvar		103
nonsense			7 clinvar			7
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			14 clinvar			14
Total	0	0	126	5	0	131

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014500.5	RefSeq	NP_055315.2	9	MANE Select
ENST00000218364.5	Ensembl	ENSP00000218364.4	9	MANE Select
NM_001163280.2	RefSeq	NP_001156752.1	9	Standard
ENST00000425695.5	Ensembl	ENSP00000412420.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
viral genome replication
regulation of DNA-templated transcription, elongation

Molecular Function

RNA binding

Cellular Component

nucleus
nucleoplasm
U2-type spliceosomal complex
U2 snRNP

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000535601
Coding exons: 9
Length: 15268
Individuals with no LoFs: 125650
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125653
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.98	177	268	0.659	0.0000195	5078
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000077	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000025	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.725

Gene Damage Prediction

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