GPBP1

GC-rich promoter binding protein 1

Basic information

Region (hg38): 5:57173948-57264679

Links

ENSG00000062194 ∙ NCBI:65056 ∙ OMIM:608412 ∙ HGNC:29520 ∙ Uniprot:Q86WP2 ∙ 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 GPBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPBP1 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			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	28	1	0

Variants in GPBP1

This is a list of pathogenic ClinVar variants found in the GPBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-57214179-C-G		not specified	Uncertain significance (Aug 19, 2023)
5-57230898-G-A		not specified	Uncertain significance (Feb 06, 2023)
5-57230901-A-G		not specified	Uncertain significance (Feb 10, 2025)
5-57230957-C-T		not specified	Uncertain significance (Nov 17, 2023)
5-57230958-G-A		not specified	Uncertain significance (Dec 17, 2024)
5-57231101-A-T		not specified	Uncertain significance (Jan 23, 2025)
5-57231119-A-G		not specified	Uncertain significance (Jan 01, 2025)
5-57231236-G-A		not specified	Uncertain significance (Dec 03, 2024)
5-57231242-A-C		not specified	Uncertain significance (Mar 01, 2024)
5-57236017-G-A		not specified	Uncertain significance (Aug 08, 2023)
5-57236021-C-A		not specified	Uncertain significance (Apr 07, 2023)
5-57246387-C-T		not specified	Uncertain significance (Sep 06, 2022)
5-57246405-C-T		not specified	Uncertain significance (Dec 11, 2023)
5-57246434-C-G		not specified	Uncertain significance (Jan 05, 2022)
5-57246446-A-G		not specified	Uncertain significance (May 05, 2023)
5-57246470-G-C		not specified	Uncertain significance (Jul 17, 2024)
5-57247102-G-A		not specified	Uncertain significance (Nov 08, 2022)
5-57247147-G-A		not specified	Uncertain significance (Jul 26, 2022)
5-57247208-T-G		not specified	Uncertain significance (Jul 26, 2021)
5-57249441-C-G		not specified	Uncertain significance (Mar 11, 2024)
5-57249536-A-G		not specified	Uncertain significance (Jan 23, 2023)
5-57249538-G-C		not specified	Uncertain significance (Feb 19, 2025)
5-57249545-A-G		not specified	Uncertain significance (Aug 01, 2024)
5-57249559-C-T		not specified	Uncertain significance (Jun 22, 2021)
5-57249560-G-A		not specified	Likely benign (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPBP1	protein_coding	protein_coding	ENST00000264779	11	90732

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.416	0.584	125723	0	11	125734	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	210	263	0.797	0.0000144	3191
Missense in Polyphen		32	66.301	0.48265		902
Synonymous	-1.38	105	88.5	1.19	0.00000468	867
Loss of Function	3.76	6	27.1	0.221	0.00000156	319

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000619	0.0000619
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000629	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000717	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a GC-rich promoter-specific transactivating transcription factor. {ECO:0000250|UniProtKB:Q6NXH3}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.480
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.31

Haploinsufficiency Scores

• pHI: 0.843
• hipred: Y
• hipred_score: 0.591
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.861

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpbp1

Gene ontology

• Biological process: transcription, DNA-templated;regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated
• Cellular component: nucleus;cytosol;plasma membrane;intracellular membrane-bounded organelle
• Molecular function: DNA binding;DNA-binding transcription factor activity;protein binding