RIMKLB

ribosomal modification protein rimK like family member B

Basic information

Region (hg38): 12:8681600-8783095

Previous symbols: [ "FAM80B" ]

Links

ENSG00000166532NCBI:57494OMIM:614054HGNC:29228Uniprot:Q9ULI2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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
11
clinvar
11
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 11 0 0

Variants in RIMKLB

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

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

Position Type Phenotype Significance ClinVar
12-8713870-T-C not specified Uncertain significance (Sep 26, 2023)3154358
12-8713939-G-C not specified Uncertain significance (Mar 31, 2022)2358442
12-8714033-G-C not specified Uncertain significance (Mar 19, 2024)3314351
12-8749864-C-A not specified Uncertain significance (Feb 03, 2022)2275400
12-8749889-C-G not specified Uncertain significance (Jul 25, 2023)2593576
12-8749933-G-A not specified Uncertain significance (Aug 04, 2023)2616390
12-8752005-A-C not specified Uncertain significance (Jun 24, 2022)2295827
12-8752013-A-G not specified Uncertain significance (Mar 29, 2024)3314350
12-8773429-A-G not specified Uncertain significance (Sep 25, 2023)3154359
12-8773435-G-T not specified Uncertain significance (May 23, 2024)3314352
12-8773615-C-T not specified Uncertain significance (Dec 06, 2021)2221481
12-8773642-C-T not specified Uncertain significance (Sep 29, 2022)2359364
12-8773702-G-A not specified Uncertain significance (Feb 21, 2024)3154357
12-8773759-A-G not specified Uncertain significance (Jul 27, 2021)2389901

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RIMKLBprotein_codingprotein_codingENST00000357529 5101496
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.5930.407124784091247930.0000361
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.341312310.5670.00001392527
Missense in Polyphen2768.2510.3956836
Synonymous0.004688787.10.9990.00000512787
Loss of Function2.98315.80.1900.00000101164

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001230.000123
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00009280.0000928
European (Non-Finnish)0.00003540.0000353
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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