ERC1

ELKS/RAB6-interacting/CAST family member 1

Basic information

Region (hg38): 12:990509-1495933

Previous symbols: [ "RAB6IP2" ]

Links

ENSG00000082805 ∙ NCBI:23085 ∙ OMIM:607127 ∙ HGNC:17072 ∙ Uniprot:Q8IUD2 ∙ 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 ERC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERC1 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				3	3	6
missense			41	2	6	49
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1	1	2
non coding				1		1
Total	0	1	42	6	9

Variants in ERC1

This is a list of pathogenic ClinVar variants found in the ERC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-1027920-G-A		not specified	Uncertain significance (May 31, 2023)
12-1027951-G-C		ERC1-related disorder	Benign (Jun 17, 2019)
12-1027967-C-T		not specified	Uncertain significance (Feb 12, 2024)
12-1027988-C-T		not specified	Uncertain significance (Sep 22, 2023)
12-1028028-C-T		not specified	Uncertain significance (Dec 07, 2021)
12-1028051-A-G		ERC1-related disorder	Benign (May 28, 2019)
12-1028163-G-T		not specified	Uncertain significance (Jan 03, 2024)
12-1028200-T-G		ERC1-related disorder	Likely benign (Nov 01, 2021)
12-1028203-C-T		ERC1-related disorder	Likely benign (Feb 22, 2019)
12-1028211-G-A		not specified	Uncertain significance (Mar 30, 2024)
12-1028211-G-C		ERC1-related disorder	Likely benign (Dec 28, 2022)
12-1028226-G-A		not specified	Uncertain significance (Jan 07, 2022)
12-1028267-A-G		not specified	Uncertain significance (Sep 06, 2022)
12-1028423-G-A		not specified	Uncertain significance (Jan 24, 2023)
12-1028450-A-G		not specified	Uncertain significance (Jul 09, 2021)
12-1028498-G-A		not specified	Uncertain significance (May 02, 2024)
12-1083303-T-A		not specified	Uncertain significance (Apr 25, 2023)
12-1083447-G-A		not specified	Uncertain significance (Apr 20, 2024)
12-1083520-C-T		ERC1-related disorder	Likely benign (Feb 25, 2019)
12-1083521-G-A		not specified	Uncertain significance (Jun 07, 2023)
12-1104760-G-A		not specified	Uncertain significance (Jan 31, 2024)
12-1104765-T-G		not specified	Uncertain significance (Mar 01, 2023)
12-1110205-C-G		not specified	Uncertain significance (Oct 21, 2021)
12-1110209-T-A		ERC1-related disorder	Benign (Dec 31, 2019)
12-1110274-G-A		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERC1	protein_coding	protein_coding	ENST00000397203	18	505425

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-7	1.00	125692	0	56	125748	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	510	611	0.834	0.0000344	7407
Missense in Polyphen		230	294.15	0.78192		3537
Synonymous	-1.34	246	221	1.11	0.0000117	2048
Loss of Function	4.43	23	60.0	0.383	0.00000353	691

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000242
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000707	0.000707
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000266	0.000264
Middle Eastern	0.000707	0.000707
South Asian	0.0000996	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit of the IKK complex. Probably recruits IkappaBalpha/NFKBIA to the complex. May be involved in the organization of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. May be involved in vesicle trafficking at the CAZ. May be involved in Rab-6 regulated endosomes to Golgi transport. {ECO:0000269|PubMed:15218148}.
• Pathway: NF-kappa B signaling pathway - Homo sapiens (human);Integrated Lung Cancer Pathway;Canonical NF-kappaB pathway;IL1-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.233

Intolerance Scores

• loftool: 0.323
• rvis_EVS: -0.88
• rvis_percentile_EVS: 10.54

Haploinsufficiency Scores

• pHI: 0.236
• hipred: Y
• hipred_score: 0.744
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.610

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Erc1
• 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; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;I-kappaB phosphorylation;multicellular organism development;protein transport;retrograde transport, endosome to Golgi;negative regulation of apoptotic process;positive regulation of NF-kappaB transcription factor activity
• Cellular component: Golgi membrane;cytoplasm;IkappaB kinase complex;presynaptic membrane;synapse;presynaptic active zone
• Molecular function: protein binding;Rab GTPase binding;PDZ domain binding;leucine zipper domain binding;cadherin binding