ABT1

activator of basal transcription 1, the group of SSU processome

Basic information

Region (hg38): 6:26596953-26600739

Links

ENSG00000146109

∙ NCBI:29777 ∙ OMIM:618750 ∙ HGNC:17369 ∙ Uniprot:Q9ULW3 ∙ 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 ABT1 gene.

not_specified (42 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000013375.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			42 clinvar			42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	42	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABT1	protein_coding	protein_coding	ENST00000274849	3	3099

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0203	0.911	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.174	187	194	0.965	0.0000132	1743
Missense in Polyphen		56	81.149	0.69009		718
Synonymous	-0.576	78	71.8	1.09	0.00000411	576
Loss of Function	1.55	4	9.02	0.444	3.82e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00111	0.00109
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000198	0.000185
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Could be a novel TATA-binding protein (TBP) which can function as a basal transcription activator. Can act as a regulator of basal transcription for class II genes (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

loftool: 0.335
rvis_EVS: -0.27
rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

pHI: 0.370
hipred: N
hipred_score: 0.294
ghis: 0.557

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.699

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Abt1
Phenotype

Gene ontology

Biological process: endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA);endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;spinal cord motor neuron differentiation;small-subunit processome assembly;positive regulation of nucleic acid-templated transcription
Cellular component: nucleus;transcription factor complex;nucleolus
Molecular function: DNA binding;transcription coactivator activity;RNA binding;protein binding