RIDA

reactive intermediate imine deaminase A homolog

Basic information

Region (hg38): 8:98102344-98117171

Previous symbols: [ "HRSP12" ]

Links

ENSG00000132541 ∙ NCBI:10247 ∙ OMIM:602487 ∙ HGNC:16897 ∙ Uniprot:P52758 ∙ 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 RIDA gene.

Variants pathogenicity by type

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

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIDA	protein_coding	protein_coding	ENST00000254878	6	14898

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0679	0.877	125724	0	13	125737	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0945	71	73.3	0.969	0.00000342	875
Missense in Polyphen		16	18.609	0.85981		273
Synonymous	1.32	17	25.5	0.667	0.00000117	276
Loss of Function	1.62	3	7.94	0.378	3.34e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000492	0.000492
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the hydrolytic deamination of enamine/imine intermediates that form during the course of normal metabolism. May facilitate the release of ammonia from these potentially toxic reactive metabolites, reducing their impact on cellular components. It may act on enamine/imine intermediates formed by several types of pyridoxal-5'-phosphate-dependent dehydratases including L-threonine dehydratase. {ECO:0000269|PubMed:20817725, ECO:0000269|PubMed:22094463}.
• Pathway: Metabolism of amino acids and derivatives;Metabolism;Threonine catabolism (Consensus)

Recessive Scores

• pRec: 0.167

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.332
• ghis: 0.547

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Rida

Gene ontology

• Biological process: kidney development;brain development;negative regulation of translation;L-threonine catabolic process to glycine;lung development;response to lipid;negative regulation of epithelial cell proliferation;G1 to G0 transition;RNA phosphodiester bond hydrolysis, endonucleolytic;organonitrogen compound catabolic process;response to salt
• Cellular component: nucleus;cytoplasm;mitochondrial matrix;peroxisome;cytosol;extracellular exosome
• Molecular function: RNA binding;endoribonuclease activity, producing 3'-phosphomonoesters;deaminase activity;long-chain fatty acid binding;protein homodimerization activity;transition metal ion binding;platinum binding;xenon atom binding