RTN2

reticulon 2

Basic information

Region (hg38): 19:45485293-45497055

Previous symbols: [ "SPG12" ]

Links

ENSG00000125744 ∙ NCBI:6253 ∙ OMIM:603183 ∙ HGNC:10468 ∙ Uniprot:O75298 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spastic paraplegia 12, autosomal dominant	AD	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	10677333; 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	35	7	46
missense			96	13	2	111
nonsense	1	4				5
start loss				1		1
frameshift		4	2			6
inframe indel			2			2
splice donor/acceptor (+/-2bp)		2	1			3
splice region			7	7	2	16
non coding			6	14	16	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)
19-45485408-C-G		Hereditary spastic paraplegia 12	Uncertain significance (Jan 13, 2018)
19-45485438-G-A		Hereditary spastic paraplegia 12	Uncertain significance (Jan 12, 2018)
19-45485491-C-T		Spastic paraplegia, autosomal dominant	Uncertain significance (Jun 14, 2016)
19-45485560-C-T		Hereditary spastic paraplegia 12	Uncertain significance (Jan 12, 2018)
19-45485657-A-G		Hereditary spastic paraplegia 12	Likely benign (Jan 13, 2018)
19-45485713-CGGCTTT-C		Spastic paraplegia	Uncertain significance (Feb 21, 2023)
19-45485716-C-T		Spastic paraplegia • Hereditary spastic paraplegia 12 • Inborn genetic diseases	Conflicting classifications of pathogenicity (Jul 10, 2023)
19-45485722-C-A		Spastic paraplegia	Uncertain significance (Nov 27, 2023)
19-45485728-A-G		Spastic paraplegia • Hereditary spastic paraplegia 12	Uncertain significance (Dec 25, 2022)
19-45485739-G-A		Hereditary spastic paraplegia 12 • Spastic paraplegia • RTN2-related disorder	Likely benign (Jul 28, 2023)
19-45485741-G-A		Spastic paraplegia	Likely benign (Jan 28, 2020)
19-45485753-G-A		Spastic paraplegia, autosomal dominant • Spastic paraplegia • not specified • Hereditary spastic paraplegia	Benign/Likely benign (Jan 19, 2024)
19-45485761-C-T		Spastic paraplegia • Inborn genetic diseases	Uncertain significance (Jun 16, 2023)
19-45485774-G-A		Spastic paraplegia	Likely benign (Oct 29, 2018)
19-45485782-C-A		RTN2-related disorder	Uncertain significance (Apr 20, 2023)
19-45485786-G-C		Spastic paraplegia	Uncertain significance (Mar 26, 2023)
19-45485789-C-T		Spastic paraplegia	Uncertain significance (Sep 30, 2021)
19-45486076-T-C		Spastic paraplegia	Uncertain significance (Oct 09, 2019)
19-45486090-C-T		Spastic paraplegia	Likely benign (Mar 09, 2021)
19-45486104-C-T		not specified	Uncertain significance (Feb 07, 2024)
19-45486105-G-A		Spastic paraplegia	Likely benign (Mar 03, 2023)
19-45486215-G-T			Benign (Jun 14, 2018)
19-45486231-C-G			Likely benign (May 23, 2021)
19-45488378-G-C			Benign (Jun 14, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTN2	protein_coding	protein_coding	ENST00000245923	11	11773

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.416	0.584	125740	0	5	125745	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.701	306	343	0.893	0.0000224	3403
Missense in Polyphen		90	110.9	0.81151		1091
Synonymous	0.725	144	155	0.926	0.0000103	1214
Loss of Function	4.05	7	31.5	0.222	0.00000206	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.0000548	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

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

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

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