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GeneBe

RTN2

reticulon 2

Basic information

Region (hg38): 19:45485293-45497055

Previous symbols: [ "SPG12" ]

Links

ENSG00000125744NCBI:6253OMIM:603183HGNC:10468Uniprot:O75298AlphaFoldGenCCjaxSfariGnomADPubmed

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 (128 variants)
  • not provided (60 variants)
  • Hereditary spastic paraplegia 12 (29 variants)
  • not specified (22 variants)
  • Hereditary spastic paraplegia (19 variants)
  • Inborn genetic diseases (11 variants)
  • Spastic paraplegia, autosomal dominant (5 variants)
  • Diastema, dental medial (1 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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 4 30 9 43
missense 80 16 4 100
nonsense 1 5 1 7
start loss 0
frameshift 2 3 2 7
inframe indel 0
splice variant 2 7 8 2 19
non coding 6 15 16 37
Total 3 10 99 70 31

Highest pathogenic variant AF is 0.0000593

Variants in RTN2

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

Position Type Phenotype Significance ClinVar
19-45485364-G-A Hereditary spastic paraplegia 12 Uncertain significance (Jan 13, 2018)link
19-45485408-C-G Hereditary spastic paraplegia 12 Uncertain significance (Jan 13, 2018)link
19-45485438-G-A Hereditary spastic paraplegia 12 Uncertain significance (Jan 12, 2018)link
19-45485491-C-T Spastic paraplegia, autosomal dominant Uncertain significance (Jun 14, 2016)link
19-45485560-C-T Hereditary spastic paraplegia 12 Uncertain significance (Jan 12, 2018)link
19-45485657-A-G Hereditary spastic paraplegia 12 Likely benign (Jan 13, 2018)link
19-45485716-C-T Spastic paraplegia • Hereditary spastic paraplegia 12 Conflicting interpretations of pathogenicity (Jun 03, 2022)link
19-45485728-A-G Spastic paraplegia • Hereditary spastic paraplegia 12 Uncertain significance (Nov 28, 2022)link
19-45485739-G-A Hereditary spastic paraplegia 12 • Spastic paraplegia Likely benign (May 28, 2019)link
19-45485741-G-A Spastic paraplegia Likely benign (Jan 28, 2020)link
19-45485753-G-A Spastic paraplegia, autosomal dominant • Spastic paraplegia • not specified • Hereditary spastic paraplegia Benign/Likely benign (Nov 01, 2022)link
19-45485761-C-T Spastic paraplegia • Inborn genetic diseases Uncertain significance (May 11, 2022)link
19-45485774-G-A Spastic paraplegia Likely benign (Oct 29, 2018)link
19-45485789-C-T Spastic paraplegia Uncertain significance (Sep 30, 2021)link
19-45486076-T-C Spastic paraplegia Uncertain significance (Aug 24, 2021)link
19-45486090-C-T Spastic paraplegia Likely benign (Mar 09, 2021)link
19-45486105-G-A Spastic paraplegia Likely benign (Oct 21, 2022)link
19-45486215-G-T Benign (Jun 14, 2018)link
19-45486231-C-G Likely benign (May 23, 2021)link
19-45488378-G-C Benign (Jun 14, 2018)link
19-45488464-C-A Likely benign (Mar 06, 2018)link
19-45488468-C-T Hereditary spastic paraplegia 12 Uncertain significance (Jan 13, 2018)link
19-45488469-A-G Likely pathogenic (Aug 26, 2020)link
19-45488475-T-C Spastic paraplegia Uncertain significance (Sep 28, 2022)link
19-45488478-T-G Uncertain significance (Feb 28, 2018)link

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