GMEB2

glucocorticoid modulatory element binding protein 2

Basic information

Region (hg38): 20:63587602-63627101

Links

ENSG00000101216 ∙ NCBI:26205 ∙ OMIM:607451 ∙ HGNC:4371 ∙ Uniprot:Q9UKD1 ∙ 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 GMEB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GMEB2 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	2		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	0

Variants in GMEB2

This is a list of pathogenic ClinVar variants found in the GMEB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63590096-C-T		not specified	Likely benign (Oct 08, 2024)
20-63590100-C-G		not specified	Uncertain significance (Jul 30, 2024)
20-63590100-C-T		not specified	Uncertain significance (Jan 04, 2024)
20-63590115-T-C		not specified	Likely benign (Sep 30, 2024)
20-63590124-C-A		not specified	Uncertain significance (Jul 25, 2024)
20-63590138-G-A		not specified	Uncertain significance (Jun 14, 2023)
20-63590219-T-C		not specified	Uncertain significance (Jan 06, 2023)
20-63590282-G-C		not specified	Uncertain significance (Nov 13, 2024)
20-63590330-G-A		not specified	Uncertain significance (Oct 13, 2023)
20-63590331-C-T		not specified	Uncertain significance (Jun 07, 2023)
20-63590343-T-G		not specified	Uncertain significance (Jan 11, 2023)
20-63590385-C-G		not specified	Uncertain significance (Sep 17, 2021)
20-63590426-G-A		not specified	Uncertain significance (Sep 16, 2021)
20-63590457-C-T		not specified	Uncertain significance (Aug 20, 2024)
20-63590466-G-A		not specified	Uncertain significance (Jul 26, 2024)
20-63590514-C-T		not specified	Uncertain significance (Oct 25, 2024)
20-63590531-A-G		not specified	Uncertain significance (Aug 05, 2024)
20-63590569-C-T		not specified	Likely benign (Aug 12, 2022)
20-63590666-T-C		not specified	Uncertain significance (Oct 07, 2024)
20-63592046-C-G		not specified	Uncertain significance (Dec 15, 2022)
20-63592060-A-G		not specified	Uncertain significance (Jan 23, 2024)
20-63592076-T-C		not specified	Uncertain significance (Dec 27, 2023)
20-63592117-T-C		not specified	Uncertain significance (Feb 22, 2023)
20-63592535-C-T		not specified	Uncertain significance (Feb 27, 2024)
20-63592562-C-T		not specified	Uncertain significance (Aug 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GMEB2	protein_coding	protein_coding	ENST00000266068	9	39440

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00505	122776	0	1	122777	0.00000407

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.20	220	333	0.660	0.0000217	3384
Missense in Polyphen		41	113.81	0.36025		1187
Synonymous	-0.164	157	154	1.02	0.0000119	1124
Loss of Function	3.95	1	20.1	0.0498	9.88e-7	225

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)	0.00000901	0.00000901
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.08

Haploinsufficiency Scores

• pHI: 0.297
• hipred: Y
• hipred_score: 0.673
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.505

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gmeb2

Gene ontology

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