RNLS

renalase, FAD dependent amine oxidase

Basic information

Region (hg38): 10:88273863-88584530

Previous symbols: [ "C10orf59" ]

Links

ENSG00000184719 ∙ NCBI:55328 ∙ OMIM:609360 ∙ HGNC:25641 ∙ Uniprot:Q5VYX0 ∙ 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 RNLS gene.

• not provided (37 variants)
• Inborn genetic diseases (14 variants)
• Stage 5 chronic kidney disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNLS 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	1	3
missense			20	2	3	25
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				4	16	20
Total	0	0	20	9	20

Variants in RNLS

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

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

Position	Type	Phenotype	Significance	ClinVar
10-88274691-C-T			Benign (Aug 14, 2020)
10-88274730-C-T			Likely benign (Apr 24, 2019)
10-88274731-A-G			Benign (Jun 29, 2018)
10-88274788-A-T			Benign (Jul 31, 2018)
10-88275126-C-T			Benign (Jul 31, 2018)
10-88275142-C-T			Benign (Jul 31, 2018)
10-88275225-AT-A			Benign (Jul 31, 2018)
10-88285370-A-G		not specified	Uncertain significance (Jul 13, 2022)
10-88285379-A-G		not specified	Uncertain significance (Oct 12, 2021)
10-88285444-T-A			Likely benign (May 01, 2018)
10-88285463-T-A		not specified	Uncertain significance (Feb 13, 2024)
10-88285726-A-T			Benign (Jun 28, 2018)
10-88285755-G-A			Benign (Jun 28, 2018)
10-88314229-G-A			Benign (Jun 28, 2018)
10-88314248-A-G			Benign (Jun 29, 2018)
10-88314383-G-A			Benign (Jun 29, 2018)
10-88314388-A-G			Benign (Jun 29, 2018)
10-88314537-G-A			Likely benign (Aug 01, 2023)
10-88314596-G-A			Uncertain significance (Sep 27, 2022)
10-88314600-C-T			Uncertain significance (Dec 25, 2023)
10-88314624-G-A		not specified	Uncertain significance (Dec 15, 2023)
10-88314644-G-A			Benign (Jan 12, 2024)
10-88314650-T-C			Benign (Jul 19, 2022)
10-88316086-A-G		Family history	association (-)
10-88362555-T-C			Uncertain significance (Jun 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNLS	protein_coding	protein_coding	ENST00000331772	7	310667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000380	0.829	125576	1	171	125748	0.000684

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0182	185	186	0.996	0.00000922	2218
Missense in Polyphen		64	61.667	1.0378		704
Synonymous	0.508	64	69.4	0.922	0.00000345	664
Loss of Function	1.38	11	17.2	0.640	7.93e-7	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00119	0.00118
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000276	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000397	0.000396
Middle Eastern	0.000276	0.000272
South Asian	0.00272	0.00268
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the oxidation of the less abundant 1,2- dihydro-beta-NAD(P) and 1,6-dihydro-beta-NAD(P) to form beta- NAD(P)(+). The enzyme hormone is secreted by the kidney, and circulates in blood and modulates cardiac function and systemic blood pressure. Lowers blood pressure in vivo by decreasing cardiac contractility and heart rate and preventing a compensatory increase in peripheral vascular tone, suggesting a causal link to the increased plasma catecholamine and heightened cardiovascular risk. High concentrations of catecholamines activate plasma renalase and promotes its secretion and synthesis. {ECO:0000269|PubMed:15841207, ECO:0000269|PubMed:17385068, ECO:0000269|PubMed:25531177}.
• Pathway: Metabolism;Nicotinamide salvaging;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.234
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.3

Haploinsufficiency Scores

• pHI: 0.0786
• hipred: N
• hipred_score: 0.144
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0204

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnls
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: response to ischemia;negative regulation of heart rate;NAD biosynthesis via nicotinamide riboside salvage pathway;negative regulation of blood pressure;oxidation-reduction process;response to epinephrine;response to salt
• Cellular component: extracellular region;extracellular space
• Molecular function: oxidoreductase activity, acting on NAD(P)H;epinephrine binding;NADH binding;monoamine oxidase activity