RER1

retention in endoplasmic reticulum sorting receptor 1

Basic information

Region (hg38): 1:2391775-2405442

Links

ENSG00000157916 ∙ NCBI:11079 ∙ OMIM:620048 ∙ HGNC:30309 ∙ Uniprot:O15258 ∙ 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 RER1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RER1 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			20	2	1	23
Total	0	0	23	2	1

Variants in RER1

This is a list of pathogenic ClinVar variants found in the RER1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-2399502-A-G		not specified	Uncertain significance (Aug 19, 2023)
1-2399503-T-A		not specified	Uncertain significance (Sep 27, 2021)
1-2402279-C-G		not specified	Uncertain significance (Dec 22, 2023)
1-2402288-T-G		not specified	Uncertain significance (Apr 23, 2024)
1-2403116-G-A		not specified	Uncertain significance (May 31, 2024)
1-2404815-C-G		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 12, 2018)
1-2404861-T-G		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 12, 2018)
1-2404912-C-T		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 13, 2018)
1-2404928-G-A		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 13, 2018)
1-2404931-G-A		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 13, 2018)
1-2404942-C-T		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 13, 2018)
1-2404968-G-A		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 13, 2018)
1-2404984-G-T		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 12, 2018)
1-2405021-G-GC		Peroxisome biogenesis disorder 1A (Zellweger)	Uncertain significance (Jun 14, 2016)
1-2405034-C-T		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 13, 2018)
1-2405078-C-A		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 13, 2018)
1-2405080-G-C		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 12, 2018)
1-2405090-G-A		Peroxisome biogenesis disorder 6A (Zellweger)	Likely benign (Jan 13, 2018)
1-2405123-G-A		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 12, 2018)
1-2405139-G-A		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 13, 2018)
1-2405171-C-T		Peroxisome biogenesis disorder 6A (Zellweger)	Benign/Likely benign (Jan 01, 2023)
1-2405172-G-A		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 13, 2018)
1-2405267-C-T		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 12, 2018)
1-2405321-C-T		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 22, 2018)
1-2405346-C-T		Peroxisome biogenesis disorder 6A (Zellweger)	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RER1	protein_coding	protein_coding	ENST00000605895	6	13617

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.379	0.619	124792	0	3	124795	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.13	55	121	0.456	0.00000718	1288
Missense in Polyphen		14	51.964	0.26942		577
Synonymous	-1.12	60	49.9	1.20	0.00000362	377
Loss of Function	2.64	3	13.5	0.223	7.92e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.00000883	0.00000883
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the retrieval of endoplasmic reticulum membrane proteins from the early Golgi compartment. {ECO:0000250}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.0535
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.417
• hipred: Y
• hipred_score: 0.675
• ghis: 0.633

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.863

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rer1
• Phenotype: muscle 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)

Zebrafish Information Network

• Gene name: rer1
• Affected structure: retinal rod cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: protein retention in ER lumen;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;skeletal muscle acetylcholine-gated channel clustering;positive regulation of protein localization to plasma membrane
• Cellular component: endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;plasma membrane;cell surface;integral component of Golgi membrane
• Molecular function: molecular_function;acetylcholine receptor binding