ERLIN2
protein-codingER lipid raft associated 2
Gene summary
This gene encodes a member of the SPFH domain-containing family of lipid raft-associated proteins. The encoded protein is localized to lipid rafts of the endoplasmic reticulum and plays a critical role in inositol 1,4,5-trisphosphate (IP3) signaling by mediating ER-associated degradation of activated IP3 receptors. Mutations in this gene are a cause of spastic paraplegia-18 (SPG18). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]
- C8orf2
- SPFH2
- SPG18
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0700309
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0012639
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0012639
Submitter: ClinGen
*ERLIN2* was first reported in relation to autosomal dominant hereditary spastic paraplegia 18 in 2018 (Rydning SL et al., PMID:29528531). Autosomal dominant hereditary spastic paraplegia 18 is a pure or complex form of hereditary spastic paraplegia characterized by spastic paraparesis, most prominent in the lower limbs, and unsteady gait. Onset usually occurs within the first decade of life, although patients have been reported with later onset. Some patients additionally present with increased deep tendon reflexes, amyotrophy, cerebellar ataxia, flexion contractures of the knees and intellectual disability. Per criteria outlined by the ClinGen Lumping and Splitting guidelines, we found no difference in molecular mechanism, inheritance pattern and phenotypic variability between HSP18 and ALS. Therefore, both disease entities have been lumped into a single curation under the term hereditary spastic paraplegia 18 for the purpose of this curation. It is recognized that HSP18 can convert to ALS. Autosomal recessive hereditary spastic paraplegia 18 has been curated separately. Seven variants, all missense, that have been reported in nine probands in seven publications (PMIDs:32042907, 34734492, 32094424, 34536826, 32147972, 29528531, 38607533) are included in this curation. The mechanism of pathogenicity appears to be loss of function. This gene-disease relationship is also supported by a mouse model that demonstrates that an autosomal dominant missense variant in *ERLIN2* disrupts axonogenesis in the mouse (PMID:37752894). Limited points are awarded to this evidence because it does not recapitulate the human phenotype but does demonstrate *ERLIN2* having a role in a relevant pathway. In summary, there is limited evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the ClinGen ClinGen Amyotrophic Lateral Sclerosis Spectrum Disorders GCEP on the meeting date Name of April 24, 2025 (SOP Version 11).
Inheritance Pattern: AD
Disease ID:MONDO:0957788
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0700309
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0012639
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0011663
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0012639
Submitter: ClinGen
*ERLIN2* was first reported in relation to autosomal recessive hereditary spastic paraplegia 18 in 2011 (Alazami AM et al., PMID:21796390). Autosomal recessive hereditary spastic paraplegia 18 is a pure or complex form of hereditary spastic paraplegia characterized by spastic paraparesis, most prominent in the lower limbs, and unsteady gait. Onset usually occurs within the first decade of life, although patients have been reported with later onset. Some patients additionally present with increased deep tendon reflexes, amyotrophy, cerebellar ataxia, flexion contractures of the knees and intellectual disability. Per criteria outlined by the ClinGen Lumping and Splitting guidelines, we found no difference in molecular mechanism, inheritance pattern and phenotypic variability between HSP18 and ALS. Therefore, both disease entities have been lumped into a single curation under the term hereditary spastic paraplegia 18 for the purpose of this curation. It is recognized that HSP18 can convert to ALS. Autosomal dominant hereditary spastic paraplegia 18 has been curated separately. Eight variants (4 missense, 2 splice site, 2 frameshift) that have been reported in ten probands in eight publications (PMIDs: 28832565, 32147972, 27824013, 21796390, 23109145, 23085305, 21330303, 32042907) are included in this curation. Ample segregation data is available with variants in *ERLIN2* segregating in 16 individuals across four families resulting in a summed LOD score of 14.7. More evidence may be available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. The mechanism of pathogenicity appears to be loss of function. In summary, there is definitive evidence supporting the relationship between *ERLIN2* and autosomal recessive hereditary spastic paraplegia 18. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time.This classification was approved by the ClinGen Amyotrophic Lateral Sclerosis Spectrum Disorders GCEP on the meeting date Name of Month, Date, 2025 (SOP Version 11).
Inheritance Pattern: AR
Disease ID:MONDO:0012639
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0017232
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Neurologic
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ERLIN2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_007175.8. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 2 | 37 | 2 | 42 | |
| missense | 5 | 10 | 81 | 1 | 97 | |
| nonsense | 4 | 4 | ||||
| start loss | 0 | |||||
| frameshift | 8 | 4 | 1 | 13 | ||
| splice donor/acceptor (+/-2bp) | 2 | 4 | 6 | |||
| Total | 20 | 18 | 84 | 38 | 2 | 162 |
Highest pathogenic variant AF is 0.000017969696
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_009106.1 | 11 | MANE Select | |
| Ensembl | ENSP00000428112.1 | 11 | MANE Select | |
| RefSeq | NP_001003790.1 | 6 | Standard | |
| RefSeq | NP_001003791.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Disorders of transmembrane transporters
- Disease
- Defective CFTR causes cystic fibrosis
- Transport of small molecules
- ABC-family proteins mediated transport
Biological Process
- cholesterol metabolic process
- peptidyl-tyrosine phosphorylation
- ubiquitin-dependent ERAD pathway
- SREBP signaling pathway
- negative regulation of cholesterol biosynthetic process
Molecular Function
- protein tyrosine kinase activity
- protein binding
- cholesterol binding
- ubiquitin protein ligase binding
Cellular Component
- endoplasmic reticulum
- endoplasmic reticulum membrane
- cytosol
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000276461
- Coding exons
- 11
- Length
- 22503
- Individuals with no LoFs
- 125732
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 16
- Defined
- 125748
- p
- 0.0000636
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.88 | 108 | 179 | 0.605 | 0.00000982 | 2243 |
| Missense (PolyPhen) | 41 | 79.171 | 0.51787 | 1001 | ||
| Synonymous | 0.350 | 66 | 69.7 | 0.947 | 0.00000441 | 627 |
| Loss of Function | 2.08 | 8 | 17.3 | 0.462 | 7.66e-7 | 237 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000053 | 0.000053 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the ERLIN1/ERLIN2 complex which mediates the endoplasmic reticulum-associated degradation (ERAD) of inositol 1,4,5-trisphosphate receptors (IP3Rs) such as ITPR1 (PubMed:19240031, PubMed:17502376). Promotes sterol-accelerated ERAD of HMGCR probably implicating an AMFR/gp78-containing ubiquitin ligase complex (PubMed:21343306). Involved in regulation of cellular cholesterol homeostasis by regulation the SREBP signaling pathway. May promote ER retention of the SCAP-SREBF complex (PubMed:24217618). {ECO:0000269|PubMed:17502376, ECO:0000269|PubMed:19240031, ECO:0000269|PubMed:21343306, ECO:0000269|PubMed:24217618}.;
Recessive Scores
- pRec
- 0.116
Intolerance Scores
- LoFtool
- 0.253
- RVIS EVS
- -0.49
- RVIS percentile EVS
- 22.09
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.712
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |