ERC2

ELKS/RAB6-interacting/CAST family member 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 3:55508311-56469095

Links

ENSG00000187672 ∙ NCBI:26059 ∙ OMIM:617250 ∙ HGNC:31922 ∙ Uniprot:O15083 ∙ 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 ERC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERC2 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				1		1
missense			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	0

Variants in ERC2

This is a list of pathogenic ClinVar variants found in the ERC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-55699385-G-A		not specified	Uncertain significance (Sep 01, 2021)
3-55734808-C-T		not specified	Uncertain significance (May 10, 2024)
3-55888391-C-T		not specified	Uncertain significance (Apr 04, 2024)
3-55888428-A-C		not specified	Uncertain significance (Nov 09, 2021)
3-55888428-A-G		not specified	Uncertain significance (Apr 25, 2022)
3-55888506-A-T		not specified	Uncertain significance (Jun 10, 2024)
3-55888548-A-G		not specified	Uncertain significance (Mar 28, 2022)
3-55950432-T-G		not specified	Uncertain significance (Oct 04, 2022)
3-55992067-C-T		not specified	Uncertain significance (Feb 02, 2024)
3-55992160-C-T		not specified	Uncertain significance (Jul 13, 2022)
3-55992161-G-C		not specified	Uncertain significance (Apr 19, 2024)
3-55992187-C-T		not specified	Uncertain significance (Mar 13, 2023)
3-55992190-G-A		not specified	Uncertain significance (Apr 22, 2022)
3-55992223-T-C		not specified	Uncertain significance (Feb 14, 2023)
3-56007214-C-A		not specified	Uncertain significance (Oct 25, 2022)
3-56010508-C-G		not specified	Uncertain significance (Aug 11, 2022)
3-56010520-A-T		not specified	Uncertain significance (Jul 13, 2022)
3-56010537-C-T		not specified	Uncertain significance (Mar 16, 2024)
3-56010543-C-T		not specified	Uncertain significance (Oct 13, 2023)
3-56010573-C-T		not specified	Uncertain significance (Nov 18, 2022)
3-56018952-G-A		not specified	Uncertain significance (Jan 20, 2023)
3-56080870-T-C		not specified	Uncertain significance (Jun 22, 2023)
3-56139656-T-G		not specified	Uncertain significance (Jan 23, 2024)
3-56139660-T-C		not specified	Uncertain significance (Jan 27, 2022)
3-56149037-G-A			Likely benign (Apr 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERC2	protein_coding	protein_coding	ENST00000288221	16	960056

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.989	0.0107	124644	0	17	124661	0.0000682

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.22	374	516	0.724	0.0000288	6342
Missense in Polyphen		128	202.52	0.63205		2584
Synonymous	-1.41	223	198	1.13	0.0000111	1752
Loss of Function	5.63	9	53.3	0.169	0.00000338	603

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000976	0.0000885
Middle Eastern	0.00	0.00
South Asian	0.0000987	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Thought to be involved in the organization of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. Seems to act together with BSN. May recruit liprin-alpha proteins to the CAZ.
• Pathway: Exercise-induced Circadian Regulation (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.733
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.86

Haploinsufficiency Scores

• pHI: 0.800
• hipred: Y
• hipred_score: 0.663
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.790

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Erc2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye 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)

Gene ontology

• Biological process: synaptic vesicle priming;maintenance of presynaptic active zone structure
• Cellular component: cytoskeleton;cell junction;growth cone;presynaptic membrane;presynaptic active zone;presynaptic active zone cytoplasmic component;glutamatergic synapse;GABA-ergic synapse
• Molecular function: protein binding;structural constituent of presynaptic active zone