RERE

arginine-glutamic acid dipeptide repeats, the group of Myb/SANT domain containing|Atrophins|GATA zinc finger domain containing

Basic information

Region (hg38): 1:8352397-8848921

Previous symbols: [ "ATN1L" ]

Links

ENSG00000142599

∙ NCBI:473 ∙ OMIM:605226 ∙ HGNC:9965 ∙ Uniprot:Q9P2R6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (Strong), mode of inheritance: AD
neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (Supportive), mode of inheritance: AD
neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (Strong), mode of inheritance: AD
complex neurodevelopmental disorder with or without congenital anomalies (Definitive), mode of inheritance: AD
neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart	AD	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Craniofacial; Genitourinary; Neurologic; Ophthalmologic	27087320

ClinVar

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

not_provided (641 variants)
Inborn_genetic_diseases (259 variants)
Neurodevelopmental_disorder_with_or_without_anomalies_of_the_brain,_eye,_or_heart (173 variants)
RERE-related_disorder (67 variants)
not_specified (30 variants)
See_cases (7 variants)
CHARGE_syndrome (1 variants)
Neurodevelopmental_disorder (1 variants)
Cerebral_visual_impairment_and_intellectual_disability (1 variants)
Autism_spectrum_disorder (1 variants)
Intellectual_disability (1 variants)
Cleft_palate (1 variants)
Developmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RERE gene is commonly pathogenic or not. These statistics are base on transcript: NM_001042681.2. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous	1 clinvar		5 clinvar	147 clinvar	27 clinvar	180
missense	6 clinvar	17 clinvar	476 clinvar	111 clinvar	11 clinvar	621
nonsense	3 clinvar	7 clinvar	2 clinvar			12
start loss						0
frameshift	10 clinvar	15 clinvar	4 clinvar			29
splice donor/acceptor (+/-2bp)		6 clinvar	4 clinvar			10
Total	20	45	491	258	38

Highest pathogenic variant AF is 0.0000087548

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RERE	protein_coding	protein_coding	ENST00000337907	22	465246

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.65e-9	125713	0	34	125747	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.03	737	909	0.810	0.0000589	10049
Missense in Polyphen		187	316.28	0.59124		3317
Synonymous	-2.83	453	383	1.18	0.0000269	3205
Loss of Function	7.11	3	64.7	0.0463	0.00000377	718

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000254	0.000182
Ashkenazi Jewish	0.000211	0.000198
East Asian	0.000111	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000379	0.000211
Middle Eastern	0.000111	0.0000544
South Asian	0.000247	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays a role as a transcriptional repressor during development. May play a role in the control of cell survival. Overexpression of RERE recruits BAX to the nucleus particularly to POD and triggers caspase-3 activation, leading to cell death. {ECO:0000269|PubMed:11331249}.;
Disease: DISEASE: Note=A chromosomal aberration involving RERE is found in the neuroblastoma cell line NGP. Translocation t(1;15)(p36.2;q24).; DISEASE: Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH) [MIM:616975]: An autosomal dominant syndrome characterized by developmental delay, intellectual disability, brain anomalies, and neurological abnormalities including seizures, hypotonia, and behavioral problems such as autism spectrum disorders. Brain anomalies include abnormalities and/or thinning of the corpus callosum, diminished white matter volume, abnormal cerebellar vermis, and ventriculomegaly. Congenital defects of the eye, heart and genitourinary system are present in half of the patients. {ECO:0000269|PubMed:27087320}. Note=The disease may be caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.139

Intolerance Scores

loftool: 0.0674
rvis_EVS: -2.63
rvis_percentile_EVS: 0.78

Haploinsufficiency Scores

pHI: 0.870
hipred: Y
hipred_score: 0.749
ghis: 0.621

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.717

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Rere
Phenotype: growth/size/body region phenotype; craniofacial phenotype; renal/urinary system phenotype; embryo phenotype; 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); normal 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); 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); hearing/vestibular/ear phenotype; vision/eye phenotype;

Zebrafish Information Network

Gene name: rerea
Affected structure: hair cell
Phenotype tag: abnormal
Phenotype quality: quality

Gene ontology

Biological process: chromatin remodeling;regulation of transcription by RNA polymerase II;NLS-bearing protein import into nucleus;cerebellar Purkinje cell layer maturation;cerebellar granule cell precursor proliferation;radial glia guided migration of Purkinje cell;branching morphogenesis of a nerve;dendrite morphogenesis;negative regulation of nucleic acid-templated transcription;positive regulation of nucleic acid-templated transcription
Cellular component: histone deacetylase complex;nucleus
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II transcription factor binding;DNA binding;chromatin binding;transcription coactivator activity;transcription corepressor activity;protein binding;poly-glutamine tract binding;zinc ion binding;sequence-specific DNA binding