ERLIN1

ER lipid raft associated 1, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 10:100150093-100186033

Previous symbols: [ "C10orf69", "SPFH1" ]

Links

ENSG00000107566 ∙ NCBI:10613 ∙ OMIM:611604 ∙ HGNC:16947 ∙ Uniprot:O75477 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary spastic paraplegia 62 (Limited), mode of inheritance: AR
• hereditary spastic paraplegia 62 (Supportive), mode of inheritance: AR
• hereditary spastic paraplegia 62 (Strong), mode of inheritance: AR
• amyotrophic lateral sclerosis (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spastic paraplegia 62, autosomal recessive	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	24482476

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ERLIN1 gene.

• Hereditary spastic paraplegia 62 (82 variants)
• not provided (29 variants)
• Hereditary spastic paraplegia (10 variants)
• Inborn genetic diseases (10 variants)
• Juvenile amyotrophic lateral sclerosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERLIN1 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	14	1	16
missense	1		40		1	42
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)	1		1			2
splice region			5	6		11
non coding			2	25	17	44
Total	2	1	44	39	19

Variants in ERLIN1

This is a list of pathogenic ClinVar variants found in the ERLIN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-100150880-T-C		Hereditary spastic paraplegia	Uncertain significance (Jan 24, 2017)
10-100150884-A-G		Hereditary spastic paraplegia	Uncertain significance (Jan 24, 2017)
10-100151918-T-C		Hereditary spastic paraplegia	Benign/Likely benign (Apr 19, 2021)
10-100152141-C-T		Hereditary spastic paraplegia 62	Uncertain significance (Sep 24, 2021)
10-100152142-T-G		Hereditary spastic paraplegia 62	Uncertain significance (Nov 29, 2022)
10-100152152-T-C		Hereditary spastic paraplegia 62	Likely benign (Apr 04, 2022)
10-100152160-C-T		Hereditary spastic paraplegia 62	Uncertain significance (Jul 19, 2022)
10-100152163-T-C		Hereditary spastic paraplegia 62	Uncertain significance (Apr 01, 2020)
10-100152212-T-C		Hereditary spastic paraplegia 62	Likely benign (Nov 05, 2021)
10-100152271-T-C		Hereditary spastic paraplegia 62	Uncertain significance (Jan 27, 2022)
10-100152285-T-C		Hereditary spastic paraplegia • not specified	Uncertain significance (Jan 02, 2024)
10-100152300-G-T		Hereditary spastic paraplegia 62	Uncertain significance (Nov 08, 2021)
10-100152304-C-A		Hereditary spastic paraplegia 62	Uncertain significance (May 15, 2022)
10-100152307-T-C		Hereditary spastic paraplegia 62	Benign (Feb 01, 2024)
10-100152322-T-G		Hereditary spastic paraplegia 62 • not specified	Uncertain significance (Apr 22, 2022)
10-100152338-C-T		Hereditary spastic paraplegia 62	Likely benign (Sep 04, 2022)
10-100152358-TG-T		Hereditary spastic paraplegia 62	Likely benign (Sep 18, 2023)
10-100152437-C-T			Benign (Mar 24, 2021)
10-100152509-C-T			Likely benign (Dec 21, 2021)
10-100152588-TA-T			Likely benign (May 12, 2021)
10-100154669-C-T			Likely benign (Jun 22, 2021)
10-100154787-T-C			Likely benign (May 27, 2021)
10-100154828-A-AT			Benign (May 20, 2021)
10-100154852-C-T		Hereditary spastic paraplegia 62	Likely benign (Oct 15, 2023)
10-100154872-G-A		Hereditary spastic paraplegia 62	Likely benign (Aug 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERLIN1	protein_coding	protein_coding	ENST00000421367	11	38241

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.178	0.822	125576	0	17	125593	0.0000677

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	115	183	0.628	0.00000912	2274
Missense in Polyphen		33	65.643	0.50272		847
Synonymous	0.237	63	65.4	0.963	0.00000338	646
Loss of Function	3.04	5	19.5	0.256	9.06e-7	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000286	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000620	0.0000617
Middle Eastern	0.000109	0.000109
South Asian	0.0000656	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the ERLIN1/ERLIN2 complex which mediates the endoplasmic reticulum-associated degradation (ERAD) of inositol 1,4,5-trisphosphate receptors (IP3Rs). Involved in regulation of cellular cholesterol homeostasis by regulation the SREBP signaling pathway. Binds cholesterol and may promote ER retention of the SCAP-SREBF complex (PubMed:24217618). {ECO:0000269|PubMed:19240031, ECO:0000269|PubMed:24217618}.
• Pathway: Disorders of transmembrane transporters;Disease;Defective CFTR causes cystic fibrosis;Transport of small molecules;ABC-family proteins mediated transport;ABC transporter disorders (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.515
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.354
• hipred: Y
• hipred_score: 0.580
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Erlin1

Gene ontology

• Biological process: cholesterol metabolic process;ubiquitin-dependent ERAD pathway;SREBP signaling pathway;negative regulation of cholesterol biosynthetic process;negative regulation of fatty acid biosynthetic process;transmembrane transport
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;protein-containing complex
• Molecular function: protein binding;cholesterol binding;ubiquitin protein ligase binding