ERLEC1

endoplasmic reticulum lectin 1, the group of MRH domain containing

Basic information

Region (hg38): 2:53787009-53833038

Previous symbols: [ "C2orf30" ]

Links

ENSG00000068912 ∙ NCBI:27248 ∙ OMIM:611229 ∙ HGNC:25222 ∙ Uniprot:Q96DZ1 ∙ 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 ERLEC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERLEC1 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			33	2		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	2	1

Variants in ERLEC1

This is a list of pathogenic ClinVar variants found in the ERLEC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-53787242-T-C		not specified	Uncertain significance (Apr 09, 2024)
2-53787298-G-C		not specified	Uncertain significance (Nov 17, 2022)
2-53787318-A-C		not specified	Uncertain significance (Dec 28, 2022)
2-53795946-A-G		not specified	Uncertain significance (Oct 30, 2023)
2-53795951-A-C		not specified	Uncertain significance (Apr 13, 2022)
2-53795955-G-T		not specified	Uncertain significance (Dec 01, 2023)
2-53795980-G-C		not specified	Uncertain significance (Mar 25, 2024)
2-53796003-G-T		not specified	Uncertain significance (Jan 09, 2024)
2-53796012-G-C		not specified	Uncertain significance (Jan 16, 2024)
2-53797585-C-G		Mandibular prognathia	Likely pathogenic (Mar 30, 2020)
2-53797585-C-T		Mandibular prognathia	Likely pathogenic (Mar 30, 2020)
2-53799052-G-A		not specified	Uncertain significance (Oct 29, 2021)
2-53799060-A-C		not specified	Uncertain significance (Aug 21, 2023)
2-53801421-C-G		not specified	Uncertain significance (Oct 13, 2023)
2-53801484-C-T		not specified	Uncertain significance (Apr 18, 2023)
2-53801511-A-T		not specified	Uncertain significance (Nov 02, 2023)
2-53801577-G-A		not specified	Uncertain significance (Nov 29, 2021)
2-53801814-T-C		not specified	Uncertain significance (Mar 20, 2023)
2-53801819-G-A			Likely benign (Jun 01, 2023)
2-53808314-A-G		not specified	Uncertain significance (Jun 02, 2023)
2-53808336-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-53808356-A-G		not specified	Likely benign (Oct 25, 2022)
2-53808366-A-G		not specified	Uncertain significance (Dec 28, 2023)
2-53808368-C-T		not specified	Uncertain significance (Nov 23, 2022)
2-53808372-T-C		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERLEC1	protein_coding	protein_coding	ENST00000185150	14	31776

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000325	0.997	125713	0	32	125745	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.640	226	255	0.887	0.0000120	3148
Missense in Polyphen		55	80.659	0.68188		965
Synonymous	-0.562	100	93.1	1.07	0.00000468	885
Loss of Function	2.64	14	29.5	0.475	0.00000135	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000376	0.000372
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000169	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.0000989	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable lectin that binds selectively to improperly folded lumenal proteins. May function in endoplasmic reticulum quality control and endoplasmic reticulum-associated degradation (ERAD) of both non-glycosylated proteins and glycoproteins. {ECO:0000269|PubMed:16531414, ECO:0000269|PubMed:18264092, ECO:0000269|PubMed:18502753}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Disorders of transmembrane transporters;Disease;Signal Transduction;Defective CFTR causes cystic fibrosis;Transport of small molecules;Hedgehog ligand biogenesis;Signaling by Hedgehog;ABC-family proteins mediated transport;Hh mutants that don,t undergo autocatalytic processing are degraded by ERAD;Hh mutants abrogate ligand secretion;ABC transporter disorders;Diseases of signal transduction (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.509
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.12

Haploinsufficiency Scores

• pHI: 0.392
• hipred: Y
• hipred_score: 0.672
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Erlec1

Gene ontology

• Biological process: ubiquitin-dependent ERAD pathway;retrograde protein transport, ER to cytosol;ERAD pathway;transmembrane transport;negative regulation of retrograde protein transport, ER to cytosol
• Cellular component: endoplasmic reticulum lumen;endoplasmic reticulum quality control compartment
• Molecular function: protein binding;unfolded protein binding