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.

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.

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						0
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	0

Variants in ABT1

This is a list of pathogenic ClinVar variants found in the ABT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-26597008-C-T		not specified	Uncertain significance (Mar 19, 2024)
6-26597040-G-A		not specified	Uncertain significance (Oct 25, 2024)
6-26597044-A-G		not specified	Uncertain significance (Mar 31, 2023)
6-26597046-A-T		not specified	Uncertain significance (Jun 01, 2023)
6-26597056-C-T		not specified	Uncertain significance (Aug 17, 2021)
6-26597106-C-T		not specified	Uncertain significance (Sep 14, 2023)
6-26597133-G-A		not specified	Uncertain significance (Jan 17, 2023)
6-26597155-G-A		not specified	Uncertain significance (Apr 19, 2023)
6-26597165-C-A		not specified	Uncertain significance (Oct 30, 2023)
6-26597917-G-A		not specified	Uncertain significance (Jul 14, 2021)
6-26597958-G-A		not specified	Uncertain significance (Aug 02, 2021)
6-26598031-G-C		not specified	Uncertain significance (Oct 05, 2023)
6-26598054-A-G		not specified	Uncertain significance (Nov 18, 2023)
6-26598287-C-G		not specified	Uncertain significance (Nov 09, 2023)
6-26598338-T-C		not specified	Uncertain significance (Apr 12, 2024)
6-26598373-G-A		not specified	Uncertain significance (Jun 21, 2021)
6-26598380-A-G		not specified	Uncertain significance (May 08, 2023)
6-26598403-C-A		not specified	Uncertain significance (Oct 12, 2021)
6-26598412-C-A		not specified	Uncertain significance (May 06, 2024)
6-26598421-G-A		not specified	Uncertain significance (Jun 16, 2023)
6-26598436-C-T		not specified	Uncertain significance (Jan 29, 2024)
6-26598449-C-G		not specified	Uncertain significance (Mar 22, 2023)
6-26598508-C-T		not specified	Uncertain significance (Feb 27, 2025)
6-26598518-G-A		not specified	Uncertain significance (Sep 04, 2024)
6-26598556-C-T		not specified	Uncertain significance (Nov 07, 2022)

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

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