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GeneBe

RTN2

reticulon 2

Basic information

Region (hg38): 19:45485293-45497055

Previous symbols: [ "SPG12" ]

Links

ENSG00000125744NCBI:6253OMIM:603183HGNC:10468Uniprot:O75298AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • hereditary spastic paraplegia 12 (Supportive), mode of inheritance: AD
  • hereditary spastic paraplegia 12 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Spastic paraplegia 12, autosomal dominantADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic10677333; 12427890; 22232211

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RTN2 gene.

  • Spastic paraplegia (141 variants)
  • not provided (68 variants)
  • Hereditary spastic paraplegia 12 (30 variants)
  • not specified (23 variants)
  • Inborn genetic diseases (23 variants)
  • Hereditary spastic paraplegia (19 variants)
  • Spastic paraplegia, autosomal dominant (5 variants)
  • RTN2-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTN2 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
4
clinvar
35
clinvar
7
clinvar
46
missense
96
clinvar
13
clinvar
2
clinvar
111
nonsense
1
clinvar
4
clinvar
5
start loss
1
clinvar
1
frameshift
4
clinvar
2
clinvar
6
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
2
clinvar
1
clinvar
3
splice region
7
7
2
16
non coding
6
clinvar
14
clinvar
16
clinvar
36
Total 1 10 111 63 25

Variants in RTN2

This is a list of pathogenic ClinVar variants found in the RTN2 region.

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

Position Type Phenotype Significance ClinVar
19-45485364-G-A Hereditary spastic paraplegia 12 Uncertain significance (Jan 13, 2018)329541
19-45485408-C-G Hereditary spastic paraplegia 12 Uncertain significance (Jan 13, 2018)329542
19-45485438-G-A Hereditary spastic paraplegia 12 Uncertain significance (Jan 12, 2018)329543
19-45485491-C-T Spastic paraplegia, autosomal dominant Uncertain significance (Jun 14, 2016)329544
19-45485560-C-T Hereditary spastic paraplegia 12 Uncertain significance (Jan 12, 2018)329545
19-45485657-A-G Hereditary spastic paraplegia 12 Likely benign (Jan 13, 2018)329546
19-45485713-CGGCTTT-C Spastic paraplegia Uncertain significance (Feb 21, 2023)2722338
19-45485716-C-T Spastic paraplegia • Hereditary spastic paraplegia 12 Conflicting classifications of pathogenicity (Jul 10, 2023)653220
19-45485722-C-A Spastic paraplegia Uncertain significance (Nov 27, 2023)2852640
19-45485728-A-G Spastic paraplegia • Hereditary spastic paraplegia 12 Uncertain significance (Dec 25, 2022)841510
19-45485739-G-A Hereditary spastic paraplegia 12 • Spastic paraplegia • RTN2-related condition Likely benign (Jul 28, 2023)893520
19-45485741-G-A Spastic paraplegia Likely benign (Jan 28, 2020)1096827
19-45485753-G-A Spastic paraplegia, autosomal dominant • Spastic paraplegia • not specified • Hereditary spastic paraplegia Benign/Likely benign (Jan 19, 2024)329547
19-45485761-C-T Spastic paraplegia • Inborn genetic diseases Uncertain significance (Jun 16, 2023)849447
19-45485774-G-A Spastic paraplegia Likely benign (Oct 29, 2018)793899
19-45485782-C-A RTN2-related condition Uncertain significance (Apr 20, 2023)2628393
19-45485786-G-C Spastic paraplegia Uncertain significance (Mar 26, 2023)2768298
19-45485789-C-T Spastic paraplegia Uncertain significance (Sep 30, 2021)938645
19-45486076-T-C Spastic paraplegia Uncertain significance (Oct 09, 2019)968137
19-45486090-C-T Spastic paraplegia Likely benign (Mar 09, 2021)1596008
19-45486105-G-A Spastic paraplegia Likely benign (Mar 03, 2023)2069241
19-45486215-G-T Benign (Jun 14, 2018)677525
19-45486231-C-G Likely benign (May 23, 2021)1326798
19-45488378-G-C Benign (Jun 14, 2018)670893
19-45488464-C-A Spastic paraplegia • RTN2-related condition Likely benign (Jul 09, 2023)704505

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RTN2protein_codingprotein_codingENST00000245923 1111773
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4160.584125740051257450.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7013063430.8930.00002243403
Missense in Polyphen90110.90.811511091
Synonymous0.7251441550.9260.00001031214
Loss of Function4.05731.50.2220.00000206293

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.00005480.0000544
Finnish0.00004680.0000462
European (Non-Finnish)0.00001780.0000176
Middle Eastern0.00005480.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Intolerance Scores

loftool
0.619
rvis_EVS
-0.2
rvis_percentile_EVS
39.11

Haploinsufficiency Scores

pHI
0.590
hipred
N
hipred_score
0.322
ghis
0.527

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.830

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rtn2
Phenotype
muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype;

Gene ontology

Biological process
regulation of glucose import;intracellular protein transmembrane transport
Cellular component
endoplasmic reticulum;terminal cisterna;integral component of endoplasmic reticulum membrane;T-tubule
Molecular function
protein binding