GMEB1

glucocorticoid modulatory element binding protein 1

Basic information

Region (hg38): 1:28668778-28719353

Links

ENSG00000162419 ∙ NCBI:10691 ∙ OMIM:604409 ∙ HGNC:4370 ∙ Uniprot:Q9Y692 ∙ 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 GMEB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GMEB1 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				1		1
missense			20			20
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	20	1	1

Variants in GMEB1

This is a list of pathogenic ClinVar variants found in the GMEB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-28690084-G-A		not specified	Uncertain significance (Jan 21, 2025)
1-28690121-C-T		not specified	Uncertain significance (Jan 09, 2024)
1-28690162-A-G		not specified	Uncertain significance (Dec 11, 2024)
1-28690203-G-GT			Benign (Oct 02, 2024)
1-28691588-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-28691602-G-A		not specified	Uncertain significance (Apr 12, 2024)
1-28691603-C-T		not specified	Uncertain significance (Jun 27, 2022)
1-28693026-C-G		not specified	Uncertain significance (Aug 01, 2024)
1-28696943-G-A		not specified	Uncertain significance (Apr 07, 2022)
1-28702443-A-G		not specified	Uncertain significance (Feb 28, 2025)
1-28702479-G-A		not specified	Uncertain significance (Sep 22, 2023)
1-28702512-G-A		not specified	Uncertain significance (Dec 24, 2024)
1-28702524-A-G		not specified	Uncertain significance (Feb 07, 2023)
1-28702531-C-T		not specified	Uncertain significance (Aug 21, 2024)
1-28704255-A-G		not specified	Uncertain significance (Jan 20, 2025)
1-28710600-C-G		not specified	Uncertain significance (Oct 28, 2023)
1-28714147-G-C		not specified	Uncertain significance (May 09, 2023)
1-28714168-A-G		not specified	Uncertain significance (Feb 01, 2025)
1-28714238-C-A		not specified	Uncertain significance (Sep 10, 2024)
1-28714287-A-G			Likely benign (Mar 01, 2023)
1-28714315-A-G		not specified	Uncertain significance (Aug 02, 2023)
1-28714391-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-28714414-G-C			Uncertain significance (Feb 01, 2023)
1-28714486-A-G		not specified	Uncertain significance (Jan 02, 2024)
1-28714543-G-T		not specified	Uncertain significance (Feb 25, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GMEB1	protein_coding	protein_coding	ENST00000294409	9	50622

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.985	0.0145	125513	0	3	125516	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.37	191	308	0.620	0.0000151	3774
Missense in Polyphen		48	108.25	0.44343		1342
Synonymous	0.506	108	115	0.940	0.00000616	1134
Loss of Function	3.91	2	21.6	0.0924	9.21e-7	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000182	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000390	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Trans-acting factor that binds to glucocorticoid modulatory elements (GME) present in the TAT (tyrosine aminotransferase) promoter and increases sensitivity to low concentrations of glucocorticoids. Binds also to the transferrin receptor promoter. Essential auxiliary factor for the replication of parvoviruses.

Intolerance Scores

• loftool: 0.253
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.222
• hipred: Y
• hipred_score: 0.825
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.884

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gmeb1

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;transcription coactivator activity;metal ion binding