GMEB1

glucocorticoid modulatory element binding protein 1

Basic information

Region (hg38): 1:28668778-28719353

Links

ENSG00000162419NCBI:10691OMIM:604409HGNC:4370Uniprot:Q9Y692AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
1
missense
20
clinvar
20
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
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)3854412
1-28690121-C-T not specified Uncertain significance (Jan 09, 2024)3100467
1-28690162-A-G not specified Uncertain significance (Dec 11, 2024)3854415
1-28690203-G-GT Benign (Oct 02, 2024)2776119
1-28691588-C-T not specified Uncertain significance (Jun 17, 2024)3281701
1-28691602-G-A not specified Uncertain significance (Apr 12, 2024)3281700
1-28691603-C-T not specified Uncertain significance (Jun 27, 2022)2355958
1-28693026-C-G not specified Uncertain significance (Aug 01, 2024)3520806
1-28696943-G-A not specified Uncertain significance (Apr 07, 2022)2281669
1-28702443-A-G not specified Uncertain significance (Feb 28, 2025)2409654
1-28702479-G-A not specified Uncertain significance (Sep 22, 2023)3100468
1-28702512-G-A not specified Uncertain significance (Dec 24, 2024)3854410
1-28702524-A-G not specified Uncertain significance (Feb 07, 2023)2481779
1-28702531-C-T not specified Uncertain significance (Aug 21, 2024)3520804
1-28704255-A-G not specified Uncertain significance (Jan 20, 2025)3854411
1-28710600-C-G not specified Uncertain significance (Oct 28, 2023)3100469
1-28714147-G-C not specified Uncertain significance (May 09, 2023)2522517
1-28714168-A-G not specified Uncertain significance (Feb 01, 2025)3854416
1-28714238-C-A not specified Uncertain significance (Sep 10, 2024)3520807
1-28714287-A-G Likely benign (Mar 01, 2023)2638580
1-28714315-A-G not specified Uncertain significance (Aug 02, 2023)2615185
1-28714391-G-A not specified Uncertain significance (Feb 28, 2023)3100465
1-28714414-G-C Uncertain significance (Feb 01, 2023)2638581
1-28714486-A-G not specified Uncertain significance (Jan 02, 2024)3100466
1-28714543-G-T not specified Uncertain significance (Feb 25, 2025)3854417

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GMEB1protein_codingprotein_codingENST00000294409 950622
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9850.0145125513031255160.0000120
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.371913080.6200.00001513774
Missense in Polyphen48108.250.443431342
Synonymous0.5061081150.9400.000006161134
Loss of Function3.91221.60.09249.21e-7275

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001820.0000176
Middle Eastern0.000.00
South Asian0.00003900.0000327
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Gmeb1
Phenotype

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