GTF2A1L

general transcription factor IIA subunit 1 like, the group of General transcription factor IIA complex subunits

Basic information

Region (hg38): 2:48617797-48733148

Links

ENSG00000242441 ∙ NCBI:11036 ∙ OMIM:605358 ∙ HGNC:30727 ∙ Uniprot:Q9UNN4 ∙ 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 GTF2A1L gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF2A1L 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in GTF2A1L

This is a list of pathogenic ClinVar variants found in the GTF2A1L region.

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

Position	Type	Phenotype	Significance	ClinVar
2-48617882-G-C		not specified	Uncertain significance (May 04, 2022)
2-48620875-G-C		not specified	Uncertain significance (Aug 12, 2021)
2-48620897-G-A		not specified	Uncertain significance (Feb 28, 2024)
2-48621216-G-A		not specified	Uncertain significance (Apr 08, 2022)
2-48621265-G-C		not specified	Uncertain significance (Sep 06, 2022)
2-48646457-C-G		not specified	Uncertain significance (Oct 29, 2021)
2-48646471-A-G		not specified	Uncertain significance (Aug 02, 2022)
2-48646471-A-T		not specified	Uncertain significance (Dec 23, 2022)
2-48646512-A-G		not specified	Uncertain significance (Dec 08, 2023)
2-48646525-C-T		not specified	Uncertain significance (Jul 19, 2022)
2-48646611-A-G		not specified	Uncertain significance (Sep 15, 2021)
2-48646648-A-G		not specified	Uncertain significance (Sep 17, 2021)
2-48646651-A-C		not specified	Uncertain significance (Jan 19, 2024)
2-48646656-G-A		not specified	Likely benign (Dec 07, 2021)
2-48646657-C-T		not specified	Uncertain significance (May 25, 2022)
2-48646675-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-48646717-T-C		not specified	Uncertain significance (Sep 14, 2022)
2-48646723-C-T		not specified	Uncertain significance (Aug 12, 2021)
2-48646731-A-G		not specified	Uncertain significance (May 16, 2023)
2-48646771-A-G		not specified	Uncertain significance (Mar 04, 2024)
2-48646873-T-G		not specified	Uncertain significance (Mar 01, 2024)
2-48646876-C-G		not specified	Uncertain significance (Jun 16, 2023)
2-48646880-A-C		not specified	Uncertain significance (Jan 09, 2023)
2-48646963-A-G		not specified	Uncertain significance (Sep 20, 2023)
2-48646978-G-A		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF2A1L	protein_coding	protein_coding	ENST00000403751	9	115351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.78e-11	0.148	124631	0	71	124702	0.000285

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.36	310	250	1.24	0.0000119	3152
Missense in Polyphen		64	67.569	0.94718		958
Synonymous	-2.45	119	89.5	1.33	0.00000473	905
Loss of Function	0.611	18	21.0	0.856	9.56e-7	263

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00128	0.00128
Ashkenazi Jewish	0.00	0.00
East Asian	0.000870	0.000870
Finnish	0.00	0.00
European (Non-Finnish)	0.000203	0.000197
Middle Eastern	0.000870	0.000870
South Asian	0.000133	0.000131
Other	0.000340	0.000327

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a testis specific transcription factor. Binds DNA in conjunction with GTF2A2 and TBP (the TATA-binding protein) and together with GTF2A2, allows mRNA transcription. {ECO:0000269|PubMed:10364255}.
• Pathway: Basal transcription factors - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.439
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.45

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.196
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Gtf2a1l

Gene ontology

• Biological process: transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;cognition;positive regulation of nucleic acid-templated transcription
• Cellular component: transcription factor TFIIA complex;cytoplasm
• Molecular function: DNA binding;transcription coactivator activity;protein binding