GREB1

growth regulating estrogen receptor binding 1

Basic information

Region (hg38): 2:11482340-11642788

Links

ENSG00000196208 ∙ NCBI:9687 ∙ OMIM:611736 ∙ HGNC:24885 ∙ Uniprot:Q4ZG55 ∙ 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 GREB1 gene.

• Inborn genetic diseases (79 variants)
• not provided (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GREB1 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				8	3	11
missense			77	3	3	83
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	77	11	6

Variants in GREB1

This is a list of pathogenic ClinVar variants found in the GREB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-11556630-G-T		not specified	Uncertain significance (Dec 16, 2023)
2-11556652-G-A		not specified	Uncertain significance (Nov 17, 2022)
2-11556694-G-A		not specified	Uncertain significance (Apr 20, 2023)
2-11562526-G-A		not specified	Uncertain significance (May 24, 2023)
2-11576392-T-A		not specified	Uncertain significance (Nov 03, 2022)
2-11578289-C-A			Benign (Aug 05, 2018)
2-11578363-C-T		not specified	Uncertain significance (Feb 17, 2023)
2-11578380-G-A		not specified	Uncertain significance (Oct 04, 2022)
2-11578428-G-A		not specified	Uncertain significance (Jan 04, 2024)
2-11580745-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-11580760-G-A			Benign (Jun 29, 2018)
2-11580774-G-A			Benign (Jul 13, 2018)
2-11580821-C-G		not specified	Uncertain significance (Jun 29, 2023)
2-11585168-G-A			Likely benign (Jul 01, 2022)
2-11585177-C-T			Likely benign (Oct 01, 2022)
2-11585203-G-A		not specified	Uncertain significance (May 31, 2023)
2-11585205-T-C		not specified	Uncertain significance (Dec 01, 2022)
2-11585767-G-A		not specified	Likely benign (Jan 31, 2024)
2-11585767-G-T		not specified	Uncertain significance (Jan 03, 2022)
2-11585786-C-T		not specified	Uncertain significance (Dec 14, 2023)
2-11585803-G-A		not specified	Uncertain significance (Jun 05, 2023)
2-11588802-C-G		not specified	Uncertain significance (Feb 06, 2023)
2-11588803-T-G		not specified	Uncertain significance (Sep 27, 2022)
2-11588812-C-T		not specified	Uncertain significance (Nov 21, 2022)
2-11588835-G-A		not specified	Likely benign (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GREB1	protein_coding	protein_coding	ENST00000381486	32	108673

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.60e-9	1.00	125686	0	62	125748	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.68	1022	1.18e+3	0.862	0.0000764	12657
Missense in Polyphen		374	507.65	0.73672		5428
Synonymous	-0.693	562	541	1.04	0.0000406	3930
Loss of Function	5.62	31	87.9	0.353	0.00000419	1012

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000348	0.000333
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000225	0.000217
Finnish	0.000371	0.000370
European (Non-Finnish)	0.000308	0.000299
Middle Eastern	0.000225	0.000217
South Asian	0.000265	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in estrogen-stimulated cell proliferation. Acts as a regulator of hormone-dependent cancer growth in breast and prostate cancers.
• Pathway: Ectoderm Differentiation;Signal Transduction;downregulated of mta-3 in er-negative breast tumors;Signaling by Nuclear Receptors;Estrogen-dependent gene expression;ESR-mediated signaling;Validated nuclear estrogen receptor alpha network (Consensus)

Intolerance Scores

• loftool: 0.471
• rvis_EVS: -0.05
• rvis_percentile_EVS: 48.93

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.685
• ghis: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.471

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Greb1
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Cellular component: nucleoplasm;integral component of membrane;extracellular exosome