GREB1L

GREB1 like retinoic acid receptor coactivator

Basic information

Region (hg38): 18:21242232-21526112

Previous symbols: [ "KIAA1772" ]

Links

ENSG00000141449 ∙ NCBI:80000 ∙ OMIM:617782 ∙ HGNC:31042 ∙ Uniprot:Q9C091 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• renal hypodysplasia/aplasia 3 (Definitive), mode of inheritance: AD
• renal hypodysplasia/aplasia 3 (Moderate), mode of inheritance: AD
• renal hypodysplasia/aplasia 3 (Limited), mode of inheritance: AD
• renal hypodysplasia/aplasia 3 (Definitive), mode of inheritance: AD
• bilateral renal agenesis (Supportive), mode of inheritance: AR
• renal agenesis, unilateral (Supportive), mode of inheritance: AD
• renal hypodysplasia/aplasia 3 (Strong), mode of inheritance: AD
• hearing loss, autosomal dominant 80 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Renal hypodysplasia/aplasia 3; Deafness, autosomal dominant 80	AD	Audiologic/Otolaryngologic; Renal	Individuals with Renal hypodysplasia/aplasia 3 may manifest with subtle findings such as vesicoureteral reflux, and awareness may allow prophylactic measures to preserve renal function; In Deafness, autosomal dominant 80, early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Renal	28739660; 29100090; 29100091; 29955957; 32585897

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GREB1L gene.

• not_provided (277 variants)
• GREB1L-related_disorder (78 variants)
• Renal_hypodysplasia/aplasia_3 (73 variants)
• Hearing_loss,_autosomal_dominant_80 (24 variants)
• Renal_agenesis_and_hypodysplasia (11 variants)
• Mayer-Rokitansky-Kuster-Hauser_syndrome (10 variants)
• Mayer_Rokitansky_Kuster_Hauser_syndrome_type_1 (8 variants)
• Mayer-Rokitansky-K�ster-Hauser_syndrome_type_2 (8 variants)
• not_specified (6 variants)
• Renal_agenesis (3 variants)
• Anhydramnios (3 variants)
• Male_infertility_with_azoospermia_or_oligozoospermia_due_to_single_gene_mutation (2 variants)
• Scoliosis,_isolated,_susceptibility_to,_1 (2 variants)
• Short_stature (2 variants)
• Congenital_anomaly_of_kidney_and_urinary_tract (2 variants)
• Inner_ear_malformation (2 variants)
• Autosomal_dominant_nonsyndromic_hearing_loss (1 variants)
• Profound_hearing_impairment (1 variants)
• Renal_cortical_hyperechogenicity (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GREB1L gene is commonly pathogenic or not. These statistics are base on transcript: NM_001142966.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	68	6	78
missense	4	15	195	20	8	242
nonsense	9	11				20
start loss						0
frameshift	18	17	3			38
splice donor/acceptor (+/-2bp)	4	3	1			8
Total	35	46	203	88	14

Highest pathogenic variant AF is 0.0000303071

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GREB1L	protein_coding	protein_coding	ENST00000580732	31	283176

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.00e-12	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	5.37	525	1.00e+3	0.523	0.0000543	12545
Missense in Polyphen		219	458.74	0.47739		5749
Synonymous	3.78	297	392	0.757	0.0000217	3803
Loss of Function	8.30	2	84.2	0.0237	0.00000449	1078

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a major role in early metanephros and genital development. {ECO:0000269|PubMed:29100091}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: 0.87
• rvis_percentile_EVS: 88.8

Haploinsufficiency Scores

• pHI: 0.248
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Greb1l
• Phenotype: renal/urinary system phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; embryo phenotype; liver/biliary system phenotype; respiratory system phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: greb1l
• Affected structure: pronephric proximal straight tubule
• Phenotype tag: abnormal
• Phenotype quality: dilated

Gene ontology

• Biological process: metanephros development;branching involved in ureteric bud morphogenesis;kidney development;cardiac ventricle development;male genitalia development;uterus development;paramesonephric duct development;mesonephric duct development
• Cellular component: integral component of membrane