RTN1

reticulon 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 14:59595975-59870776

Previous symbols: [ "NSP" ]

Links

ENSG00000139970 ∙ NCBI:6252 ∙ OMIM:600865 ∙ HGNC:10467 ∙ Uniprot:Q16799 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RTN1 gene.

• not provided (7 variants)
• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTN1 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					2	2
missense			4	1	4	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	4	1	7

Variants in RTN1

This is a list of pathogenic ClinVar variants found in the RTN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-59603075-C-T		not specified	Uncertain significance (Jan 03, 2022)
14-59603890-A-G		not specified	Uncertain significance (Mar 29, 2022)
14-59607304-C-T		not specified	Uncertain significance (Mar 07, 2024)
14-59607391-C-T		not specified	Uncertain significance (Oct 20, 2023)
14-59727466-C-T			Benign (Jul 13, 2018)
14-59727615-T-C			Benign (Jul 26, 2018)
14-59727639-C-A		not specified	Likely benign (Jul 20, 2021)
14-59745747-C-A		not specified	Uncertain significance (Oct 05, 2021)
14-59745807-T-G		not specified	Uncertain significance (Aug 09, 2021)
14-59745908-C-T			Benign (Jul 15, 2018)
14-59745983-C-T			Benign (Dec 31, 2019)
14-59746084-G-A			Benign (Jul 23, 2018)
14-59746353-T-C			Benign (Jul 23, 2018)
14-59746427-T-C		not specified	Uncertain significance (Sep 01, 2021)
14-59746490-C-G			Benign (Jul 23, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTN1	protein_coding	protein_coding	ENST00000267484	9	274991

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.986	0.0141	125697	0	6	125703	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.950	366	421	0.870	0.0000247	4911
Missense in Polyphen		80	130.35	0.61371		1591
Synonymous	0.0381	192	193	0.997	0.0000138	1629
Loss of Function	4.19	3	26.1	0.115	0.00000111	357

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000273	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in neuroendocrine secretion or in membrane trafficking in neuroendocrine cells.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.217
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.57

Haploinsufficiency Scores

• pHI: 0.507
• hipred: Y
• hipred_score: 0.608
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.757

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rtn1

Gene ontology

• Cellular component: endoplasmic reticulum;integral component of endoplasmic reticulum membrane
• Molecular function: protein binding