HTATSF1

Summary

HTATSF1 (HIV-1 Tat specific factor 1, HGNC:5276) is a protein-coding gene on chromosome Xq26.3, encoding 17S U2 SnRNP complex component HTATSF1 (O43719). Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs. It is a common-essential gene (DepMap: required in 91.8% of cancer cell lines).

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.

Source: NCBI Gene 27336 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 141 total
• Cancer dependency (DepMap): dependent in 91.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_014500

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:5276
Approved symbol	HTATSF1
Name	HIV-1 Tat specific factor 1
Location	Xq26.3
Locus type	gene with protein product
Status	Approved
Aliases	TAT-SF1
Ensembl gene	ENSG00000102241
Ensembl biotype	protein_coding
OMIM	300346
Entrez	27336

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 15 protein_coding

ENST00000218364, ENST00000425695, ENST00000448450, ENST00000535601, ENST00000866995, ENST00000866996, ENST00000866997, ENST00000866998, ENST00000866999, ENST00000928616, ENST00000928617, ENST00000959448, ENST00000959449, ENST00000959450, ENST00000959451

RefSeq mRNA: 2 — MANE Select: NM_014500 NM_001163280, NM_014500

CCDS: CCDS14657

Canonical transcript exons

ENST00000218364 — 9 exons

Exon	Start	End
ENSE00000677003	136499598	136499778
ENSE00000677004	136500158	136500205
ENSE00000677005	136500664	136500818
ENSE00000677007	136504364	136504463
ENSE00000677008	136509091	136509180
ENSE00000677009	136510082	136510219
ENSE00001305625	136510808	136512346
ENSE00001932076	136497592	136497870
ENSE00003785219	136502778	136502941

Expression profiles

Bgee: expression breadth ubiquitous, 299 present calls, max score 99.41.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.3777 / max 485.9157, expressed in 1813 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197693	26.5144	1810
197699	2.0582	660
197698	1.5529	829
197697	1.1956	625
197694	0.5352	242
197696	0.3949	198
197695	0.1266	36

Top tissues by expression

300 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	99.41	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	98.30	gold quality
pituitary gland	UBERON:0000007	98.17	gold quality
germinal epithelium of ovary	UBERON:0001304	97.97	gold quality
medial globus pallidus	UBERON:0002477	97.91	gold quality
epithelium of nasopharynx	UBERON:0001951	97.76	gold quality
ganglionic eminence	UBERON:0004023	97.75	gold quality
nasopharynx	UBERON:0001728	97.74	gold quality
globus pallidus	UBERON:0001875	97.72	gold quality
tendon of biceps brachii	UBERON:0008188	97.69	gold quality
vastus lateralis	UBERON:0001379	97.67	gold quality
adenohypophysis	UBERON:0002196	97.67	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	97.65	gold quality
oocyte	CL:0000023	97.55	gold quality
biceps brachii	UBERON:0001507	97.49	gold quality
superior vestibular nucleus	UBERON:0007227	97.37	gold quality
medulla oblongata	UBERON:0001896	97.26	gold quality
subthalamic nucleus	UBERON:0001906	97.24	gold quality
lateral globus pallidus	UBERON:0002476	97.22	gold quality
mucosa of paranasal sinus	UBERON:0005030	97.19	gold quality
embryo	UBERON:0000922	97.15	gold quality
amniotic fluid	UBERON:0000173	97.08	gold quality
tendon	UBERON:0000043	97.04	gold quality
synovial joint	UBERON:0002217	97.02	gold quality
muscle of leg	UBERON:0001383	96.91	gold quality
cortical plate	UBERON:0005343	96.90	gold quality
gastrocnemius	UBERON:0001388	96.89	gold quality
skeletal muscle organ	UBERON:0014892	96.88	gold quality
muscle organ	UBERON:0001630	96.87	gold quality
inferior vagus X ganglion	UBERON:0005363	96.86	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-CURD-112	no	2.26
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting HTATSF1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-544A	99.84	68.66	1965
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-3923	99.52	69.21	446
HSA-MIR-20A-3P	99.44	69.10	1575
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-5589-3P	99.29	68.30	1443
HSA-MIR-194-5P	99.01	69.65	1465
HSA-MIR-4742-5P	98.89	68.41	1542
HSA-MIR-552-3P	96.68	64.12	1026
HSA-MIR-5586-5P	96.29	68.02	685

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 91.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 7)

• These results support the notion that Tat-induced neuropathogenesis is mediated by multiple mechanisms involving both intracellular and extracellular Tat protein. (PMID:15050687)
• phosphorylated by P-TEFb kinase during HIV-1 transcription in Tat/TAR dependent manner (PMID:15564463)
• Intracellular HIV-1 Tat protein represses constitutive LMP2 transcription increasing proteasome activity by interfering with the binding of IRF-1 to STAT1 (PMID:16512786)
• Tat-SF1 is not required for regulating HIV-1 transcription, but is required for maintaining the ratios of different classes of HIV-1 transcripts. (PMID:19479034)
• these findings suggest that Tat-SF1 functions independently in transcription and splicing of cellular genes. (PMID:21282347)
• This study validates Tat-SF1 as an HDF in CD4+ T cell-derived SupT1 cells. (PMID:23153325)
• Human Tat-specific factor 1 binds the HIV-1 genome and selectively transports HIV-1 RNAs. (PMID:32016635)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	htatsf1	ENSDARG00000056649
mus_musculus	Htatsf1	ENSMUSG00000067873
rattus_norvegicus	Htatsf1	ENSRNOG00000027761
drosophila_melanogaster	barc	FBGN0037081
caenorhabditis_elegans	cus-2	WBGENE00022025

Protein

Protein identifiers

17S U2 SnRNP complex component HTATSF1 — O43719 (reviewed: O43719)

Alternative names: HIV Tat-specific factor 1

All UniProt accessions (3): O43719, Q5H918, Q5H919

UniProt curated annotations — full annotation on UniProt →

Function. Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs. The 17S U2 SnRNP complex (1) directly participates in early spliceosome assembly and (2) mediates recognition of the intron branch site during pre-mRNA splicing by promoting the selection of the pre-mRNA branch-site adenosine, the nucleophile for the first step of splicing. Within the 17S U2 SnRNP complex, HTATSF1 is required to stabilize the branchpoint-interacting stem loop. HTATSF1 is displaced from the 17S U2 SnRNP complex before the stable addition of the 17S U2 SnRNP complex to the spliceosome, destabilizing the branchpoint-interacting stem loop and allowing to probe intron branch site sequences. Also acts as a regulator of transcriptional elongation, possibly by mediating the reciprocal stimulatory effect of splicing on transcriptional elongation. Involved in double-strand break (DSB) repair via homologous recombination in S-phase by promoting the recruitment of TOPBP1 to DNA damage sites. Mechanistically, HTATSF1 is (1) recruited to DNA damage sites in S-phase via interaction with poly-ADP-ribosylated RPA1 and (2) phosphorylated by CK2, promoting recruitment of TOPBP1, thereby facilitating RAD51 nucleofilaments formation and RPA displacement, followed by homologous recombination. (Microbial infection) 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.

Subunit / interactions. Component of the 17S U2 SnRNP complex, a ribonucleoprotein complex that contains small nuclear RNA (snRNA) U2 and a number of specific proteins. Within the 17S U2 SnRNP complex, interacts (via UHM region) directly with SF3B1. Component of a complex which is at least composed of HTATSF1/Tat-SF1, the P-TEFb complex components CDK9 and CCNT1, RNA polymerase II, SUPT5H, and NCL/nucleolin. Interacts with GTF2F2/RAP30 and POLR2A. Interacts with TCERG1/CA150. Interacts with (poly-ADP-ribosylated) RPA1; promoting HTATSF1 recruitment to DNA damage sites. Interacts (when phosphorylated) with TOPBP1; promoting recruitment of TOPBP1 to DNA damage sites during S-phase.

Subcellular location. Nucleus. Chromosome.

Tissue specificity. Widely expressed.

Post-translational modifications. Phosphorylation at Ser-748 by CK2 during S-phase in response to DNA damage promotes interaction with TOPBP1 and double-strand break (DSB) repair via homologous recombination.

Domain organisation. The RRM domains mediate interaction with U snRNPs. The RRM domains specifically bind poly-ADP-ribosylated RPA1.

Similarity. Belongs to the HTATSF1 family.

RefSeq proteins (2): NP_001156752, NP_055315* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR034392	TatSF1-like_RRM1	Domain
IPR034393	TatSF1-like	Family
IPR035979	RBD_domain_sf	Homologous_superfamily

Pfam: PF00076

UniProt features (84 total): modified residue 31, compositionally biased region 14, strand 9, helix 7, region of interest 6, mutagenesis site 4, sequence variant 3, domain 2, cross-link 2, sequence conflict 2, turn 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

11 structures.

PDB	Method	Resolution (Å)
6N3D	X-RAY DIFFRACTION	1.13
6N3E	X-RAY DIFFRACTION	1.89
6NSX	X-RAY DIFFRACTION	2
6N3F	X-RAY DIFFRACTION	2.1
7Q3L	ELECTRON MICROSCOPY	2.21
7EVO	ELECTRON MICROSCOPY	2.5
8HK1	ELECTRON MICROSCOPY	2.7
6Y50	ELECTRON MICROSCOPY	4.1
6Y53	ELECTRON MICROSCOPY	7.1
6Y5Q	ELECTRON MICROSCOPY	7.1
2DIT	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43719-F1	59.95	0.18

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (33): 2, 297, 387, 403, 407, 409, 445, 452, 453, 481, 485, 494, 498, 521, 529, 557, 561, 579, 597, 600 …

Mutagenesis-validated functional residues (4):

Position	Phenotype
136	loss of interaction with u snrnps.
155–156	in 4a mutant; abolished binding to poly-adp-ribosylated rpa1 and recruitment to dna damage sites; when associated with 2
297–298	in 4a mutant; abolished binding to poly-adp-ribosylated rpa1 and recruitment to dna damage sites; when associated with 1
748	impaired phosphorylation by ck2, leading to abolish interaction with topbp1.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-9770562	mRNA Polyadenylation

MSigDB gene sets: 150 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, MORF_RAD21, TGACCTY_ERR1_Q2, MORF_PSMC2, MORF_RAF1, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_UP, REACTOME_MRNA_3_END_PROCESSING, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_PROTEIN_LOCALIZATION_TO_CHROMOSOME, WTGAAAT_UNKNOWN

GO Biological Process (9): mRNA splicing, via spliceosome (GO:0000398), double-strand break repair via homologous recombination (GO:0000724), U2-type prespliceosome assembly (GO:1903241), protein localization to site of double-strand break (GO:1990166), DNA repair (GO:0006281), chromatin organization (GO:0006325), mRNA processing (GO:0006397), DNA damage response (GO:0006974), RNA splicing (GO:0008380)

GO Molecular Function (5): RNA binding (GO:0003723), chromatin-protein adaptor activity (GO:0140463), poly-ADP-D-ribose modification-dependent protein binding (GO:0160004), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (7): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U2-type spliceosomal complex (GO:0005684), U2 snRNP (GO:0005686), site of double-strand break (GO:0035861), chromosome (GO:0005694)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
mRNA Splicing	1
mRNA 3’-end processing	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
binding	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
recombinational repair	1
double-strand break repair	1
spliceosomal complex assembly	1
protein localization to chromosome	1
DNA metabolic process	1
DNA damage response	1
cellular component organization	1
mRNA metabolic process	1
cellular response to stress	1
nucleic acid binding	1
chromatin binding	1
chromatin organization	1
protein-macromolecule adaptor activity	1
ADP-D-ribose modification-dependent protein binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
spliceosomal complex	1
spliceosomal snRNP complex	1
site of DNA damage	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1352 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HTATSF1	CDK9	P50750	915
HTATSF1	CCNT1	O60563	860
HTATSF1	RBM8A	Q9Y5S9	819
HTATSF1	HEXIM1	O94992	801
HTATSF1	BRD4	O60885	790
HTATSF1	TCERG1	O14776	758
HTATSF1	SUPT5H	O00267	756
HTATSF1	RPS2	P15880	751
HTATSF1	FUS	P35637	741
HTATSF1	CCNT2	O60583	708
HTATSF1	DDX46	Q7L014	667
HTATSF1	SRSF2	Q01130	622
HTATSF1	PAK1IP1	Q9NWT1	605
HTATSF1	POLR2A	P24928	604
HTATSF1	CDC40	O60508	594

IntAct

109 interactions, top by confidence:

A	B	Type	Score
SNRPF	GEMIN2	psi-mi:“MI:0914”(association)	0.910
CSNK1A1	FAM83G	psi-mi:“MI:0914”(association)	0.900
MED17	MED19	psi-mi:“MI:0914”(association)	0.840
SNRPE	GEMIN2	psi-mi:“MI:0914”(association)	0.770
SNRPD2	GEMIN2	psi-mi:“MI:0914”(association)	0.710
SNRPG	GEMIN2	psi-mi:“MI:0914”(association)	0.710
SNRPB	PRMT5	psi-mi:“MI:0914”(association)	0.670
HTATSF1	SF3B1	psi-mi:“MI:0407”(direct interaction)	0.650
HTATSF1	SF3B1	psi-mi:“MI:0915”(physical association)	0.650
SNRPA1	HTATSF1	psi-mi:“MI:0914”(association)	0.640
NCBP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
SF3B1	SAP18	psi-mi:“MI:0914”(association)	0.640
SNRPA1	U2SURP	psi-mi:“MI:0914”(association)	0.640
SF3A2	HTATSF1	psi-mi:“MI:0915”(physical association)	0.560
SNRPE	PRMT5	psi-mi:“MI:0914”(association)	0.530
SNRPN	PRMT5	psi-mi:“MI:0914”(association)	0.530
RBM7	HTATSF1	psi-mi:“MI:0914”(association)	0.530
SNRPE	SNRPGP15	psi-mi:“MI:0914”(association)	0.530
SNRPF	SNRPGP15	psi-mi:“MI:0914”(association)	0.530
TCEANC2	HTATSF1	psi-mi:“MI:0914”(association)	0.530

BioGRID (187): HTATSF1 (Affinity Capture-MS), HTATSF1 (Affinity Capture-MS), HTATSF1 (Affinity Capture-MS), PELP1 (Co-fractionation), SNRPD2 (Co-fractionation), HTATSF1 (Affinity Capture-MS), HTATSF1 (Proximity Label-MS), HTATSF1 (Biochemical Activity), HTATSF1 (Biochemical Activity), HTATSF1 (Proximity Label-MS), HTATSF1 (Affinity Capture-MS), HTATSF1 (Affinity Capture-MS), HTATSF1 (Affinity Capture-MS), HTATSF1 (Affinity Capture-MS), HTATSF1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1D9BZF0, A0A571BEE2, A6H8Y1, A8MU46, B3EWZ0, B4F777, D3YVF0, F4K4Y5, O01949, O43493, O43719, O46383, O81283, P08116, P13816, P24587, P27058, P27123, P43597, P48785, P53911, P82970, Q01033, Q10P83, Q14093, Q17Q32, Q28092, Q5H9L2, Q5MJ10, Q5RB63, Q5XHX6, Q6AXX0, Q6P902, Q6SJ82, Q84JB7, Q8BGC0, Q8IZU1, Q8VYD2, Q9D498, Q9FGW9

Diamond homologs: A2Q848, O43719, P42698, Q0CR95, Q0U1G2, Q2UK72, Q5RB63, Q8BGC0, Q8T6B9, Q94KD0, Q9N3S4, O13845, P26368, P26369, Q2HJG2, Q3UEB3, Q5R469, Q6IQE0, Q8JZX4, Q96I25, Q9UHX1, Q9WV25, F1QB54, P53830, Q27294, Q6AUG0, Q9S709, Q9ZQW8, A0A0D1DZT6, O35986, O43120, O95218, P11940, P35637, P56959, P61286, Q01844, Q19QU3, Q28009, Q5R580

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
HTATSF1	“form complex”	“U2 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 93 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Metabolism of non-coding RNA	7	63.4×	5e-10
mRNA Splicing	20	31.4×	4e-23
mRNA Splicing - Minor Pathway	9	28.8×	1e-09
Processing of Capped Intron-Containing Pre-mRNA	22	25.8×	2e-23
RNA Polymerase II Transcription Termination	8	25.1×	4e-08
snRNP Assembly	8	24.2×	5e-08
CHD1 and CHD2 subfamily	15	23.3×	4e-15
mRNA Polyadenylation	18	22.6×	5e-18

GO biological processes:

GO term	Partners	Fold	FDR
U2-type prespliceosome assembly	13	95.5×	4e-21
spliceosomal snRNP assembly	7	47.9×	2e-08
spliceosomal complex assembly	6	42.5×	6e-07
RNA splicing, via transesterification reactions	5	36.7×	2e-05
mRNA splicing, via spliceosome	23	24.8×	3e-23
RNA splicing	15	15.6×	8e-12
mRNA processing	9	8.3×	1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

141 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1392 predictions. Top by Δscore:

Variant	Effect	Δscore
X:136497856:GC:G	donor_gain	1.0000
X:136497866:CCAAG:C	donor_loss	1.0000
X:136497867:CAAG:C	donor_loss	1.0000
X:136497868:AAGG:A	donor_loss	1.0000
X:136497870:GGTA:G	donor_loss	1.0000
X:136497871:G:GA	donor_loss	1.0000
X:136497872:T:A	donor_loss	1.0000
X:136498453:GC:G	donor_gain	1.0000
X:136498454:C:CG	donor_gain	1.0000
X:136498454:C:G	donor_gain	1.0000
X:136499596:A:AG	acceptor_gain	1.0000
X:136499597:G:GG	acceptor_gain	1.0000
X:136499597:GATT:G	acceptor_gain	1.0000
X:136499648:C:CA	acceptor_gain	1.0000
X:136499774:GTCAG:G	donor_gain	1.0000
X:136499775:TCAG:T	donor_gain	1.0000
X:136499776:CAG:C	donor_gain	1.0000
X:136499777:AG:A	donor_gain	1.0000
X:136499778:GG:G	donor_gain	1.0000
X:136499779:G:GG	donor_gain	1.0000
X:136500655:A:AG	acceptor_gain	1.0000
X:136500655:AAAT:A	acceptor_gain	1.0000
X:136500656:A:AG	acceptor_gain	1.0000
X:136500657:A:AG	acceptor_gain	1.0000
X:136500657:AT:A	acceptor_gain	1.0000
X:136500658:T:A	acceptor_gain	1.0000
X:136500659:GACA:G	acceptor_loss	1.0000
X:136500662:A:AT	acceptor_loss	1.0000
X:136500662:AG:A	acceptor_gain	1.0000
X:136500663:G:GC	acceptor_loss	1.0000

AlphaMissense

5102 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:136500160:T:A	W124R	1.000
X:136500160:T:C	W124R	1.000
X:136500194:T:A	V135E	1.000
X:136500200:T:A	V137E	1.000
X:136500667:T:C	L140S	1.000
X:136500694:T:C	F149S	1.000
X:136500717:G:C	G157R	1.000
X:136500718:G:A	G157D	1.000
X:136500718:G:T	G157V	1.000
X:136500755:G:C	K169N	1.000
X:136500755:G:T	K169N	1.000
X:136500759:A:G	K171E	1.000
X:136500765:T:C	Y173H	1.000
X:136500765:T:G	Y173D	1.000
X:136500793:G:A	G182E	1.000
X:136500799:G:A	G184D	1.000
X:136500802:T:C	L185P	1.000
X:136500804:T:C	C186R	1.000
X:136500805:G:A	C186Y	1.000
X:136500806:C:G	C186W	1.000
X:136500810:T:C	Y188H	1.000
X:136500810:T:G	Y188D	1.000
X:136500818:A:C	K190N	1.000
X:136500818:A:T	K190N	1.000
X:136502794:T:C	L196P	1.000
X:136502827:G:C	R207T	1.000
X:136502845:T:A	V213D	1.000
X:136502859:T:C	F218L	1.000
X:136502859:T:G	F218V	1.000
X:136502860:T:C	F218S	1.000

dbSNP variants (sampled 300 via entrez): RS1000116066 (X:136500953 G>C), RS1000345936 (X:136506182 A>G), RS1000483190 (X:136505741 C>T), RS1000785701 (X:136496011 G>C), RS1000926116 (X:136497278 C>G,T), RS1000957013 (X:136497137 G>A,C,T), RS1001320408 (X:136499006 C>T), RS1001332653 (X:136505275 A>C), RS1001371141 (X:136495698 G>C), RS1001992634 (X:136496217 C>G), RS1002074348 (X:136506943 G>A), RS1002115914 (X:136504813 G>A,T), RS1002179163 (X:136498075 A>G), RS1002628725 (X:136504039 T>G), RS1002717947 (X:136506349 C>T)

Disease associations

OMIM: gene MIM:300346 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

47 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, decreases methylation, increases expression	3
methylmercuric chloride	increases expression	2
bisphenol A	increases expression, decreases expression, affects cotreatment	2
trichostatin A	affects cotreatment, decreases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	2
Tretinoin	decreases expression	2
FR900359	affects phosphorylation	1
TAK-243	decreases sumoylation	1
testosterone enanthate	affects expression	1
triphenyl phosphate	affects expression	1
decabromobiphenyl ether	increases expression	1
coumarin	affects phosphorylation	1
1-UFT protocol	decreases response to substance	1
di-n-butylphosphoric acid	affects expression	1
azoxystrobin	decreases expression	1
fenpyroximate	decreases expression	1
torcetrapib	increases expression	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
pyrachlostrobin	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
hexabrominated diphenyl ether 153	increases expression	1
bisphenol S	increases expression	1
LDN 193189	affects cotreatment, increases expression	1
picoxystrobin	decreases expression	1
MT19c compound	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Arsenic Trioxide	increases response to substance	1
Vorinostat	decreases expression	1
Arbutin	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.