RIMKLB

ribosomal modification protein rimK like family member B

Basic information

Region (hg38): 12:8681600-8783095

Previous symbols: [ "FAM80B" ]

Links

ENSG00000166532

∙ NCBI:57494 ∙ OMIM:614054 ∙ HGNC:29228 ∙ Uniprot:Q9ULI2 ∙ 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 RIMKLB gene.

not_specified (30 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RIMKLB gene is commonly pathogenic or not. These statistics are base on transcript: NM_001297776.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			30 clinvar			30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIMKLB	protein_coding	protein_coding	ENST00000357529	5	101496

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.593	0.407	124784	0	9	124793	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.34	131	231	0.567	0.0000139	2527
Missense in Polyphen		27	68.251	0.3956		836
Synonymous	0.00468	87	87.1	0.999	0.00000512	787
Loss of Function	2.98	3	15.8	0.190	0.00000101	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.0000354	0.0000353
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the synthesis of beta-citryl-L-glutamate and N-acetyl-L-aspartyl-L-glutamate. Beta-citryl-L-glutamate is synthesized more efficiently than N-acetyl-L-aspartyl-L-glutamate. {ECO:0000250|UniProtKB:Q80WS1}.;
Pathway: Alanine, aspartate and glutamate metabolism - Homo sapiens (human);Metabolism of amino acids and derivatives;Metabolism;Amino acid synthesis and interconversion (transamination) (Consensus)

Recessive Scores

pRec: 0.0863

Intolerance Scores

loftool: 0.272
rvis_EVS: -0.05
rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

pHI: 0.197
hipred: Y
hipred_score: 0.740
ghis: 0.463

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Rimklb
Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype;

Gene ontology

Biological process: cellular protein modification process;cellular amino acid biosynthetic process
Cellular component: cytoplasm;cytosol
Molecular function: ATP binding;metal ion binding;N-acetyl-L-aspartate-L-glutamate ligase activity;citrate-L-glutamate ligase activity