GPBP1L1

GC-rich promoter binding protein 1 like 1

Basic information

Region (hg38): 1:45627304-45688113

Links

ENSG00000159592 ∙ NCBI:60313 ∙ ∙ HGNC:28843 ∙ Uniprot:Q9HC44 ∙ 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 GPBP1L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPBP1L1 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			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	1	0

Variants in GPBP1L1

This is a list of pathogenic ClinVar variants found in the GPBP1L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-45628283-T-G		not specified	Uncertain significance (Nov 20, 2024)
1-45629589-A-G		not specified	Uncertain significance (Apr 04, 2024)
1-45629590-T-C		not specified	Uncertain significance (Sep 26, 2024)
1-45629610-T-C		not specified	Uncertain significance (May 04, 2022)
1-45629620-G-T		not specified	Uncertain significance (Jan 16, 2024)
1-45629622-G-A		not specified	Uncertain significance (Jul 16, 2024)
1-45629665-T-C		not specified	Uncertain significance (Dec 07, 2024)
1-45630537-G-A		not specified	Uncertain significance (Jul 12, 2022)
1-45630600-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-45633506-A-G		not specified	Uncertain significance (Feb 13, 2024)
1-45633583-C-T		not specified	Uncertain significance (Jul 14, 2024)
1-45633622-A-G		not specified	Uncertain significance (Apr 01, 2024)
1-45633644-G-C		not specified	Uncertain significance (Mar 31, 2023)
1-45634121-C-T		not specified	Uncertain significance (Nov 06, 2023)
1-45640238-A-G		not specified	Uncertain significance (Jan 19, 2022)
1-45640256-C-G		not specified	Uncertain significance (Apr 22, 2024)
1-45640257-T-C		not specified	Uncertain significance (Jan 31, 2024)
1-45640266-C-T		not specified	Likely benign (Feb 26, 2024)
1-45640292-T-C		not specified	Uncertain significance (Jun 07, 2024)
1-45640346-T-C		not specified	Uncertain significance (Jun 07, 2024)
1-45640350-A-G		not specified	Uncertain significance (Sep 02, 2024)
1-45640365-C-G		not specified	Uncertain significance (Aug 19, 2024)
1-45642442-G-A		not specified	Uncertain significance (May 20, 2024)
1-45642450-A-G		not specified	Uncertain significance (Apr 25, 2022)
1-45654576-C-G		not specified	Uncertain significance (Jun 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPBP1L1	protein_coding	protein_coding	ENST00000355105	10	60810

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.199	0.801	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.133	273	267	1.02	0.0000142	3127
Missense in Polyphen		90	80.303	1.1207		1059
Synonymous	-2.18	121	94.1	1.29	0.00000475	914
Loss of Function	3.44	6	24.3	0.247	0.00000136	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000196	0.000193
Middle Eastern	0.00	0.00
South Asian	0.0000332	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible transcription factor. {ECO:0000305}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.369
• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.8

Haploinsufficiency Scores

• pHI: 0.566
• hipred: N
• hipred_score: 0.465
• ghis: 0.637

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.972

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpbp1l1

Gene ontology

• Biological process: transcription, DNA-templated;regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: DNA binding;DNA-binding transcription factor activity