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GeneBe

RPL21

ribosomal protein L21, the group of L ribosomal proteins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 13:27251361-27256691

Links

ENSG00000122026NCBI:6144OMIM:603636HGNC:10313Uniprot:P46778AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • hypotrichosis simplex (Supportive), mode of inheritance: AD
  • hypotrichosis 12 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Hypotrichosis 12ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingDermatologic19751230; 21412954

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL21 gene.

  • not provided (12 variants)
  • Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL21 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
1
clinvar
1
clinvar
2
missense
2
clinvar
2
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
2
non coding
1
clinvar
6
clinvar
7
Total 0 0 2 2 7

Variants in RPL21

This is a list of pathogenic ClinVar variants found in the RPL21 region.

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

Position Type Phenotype Significance ClinVar
13-27253674-C-T Benign (Jul 14, 2018)1243002
13-27253839-A-G Likely benign (Jan 24, 2023)2842646
13-27253842-T-C Uncertain significance (Aug 11, 2023)2712009
13-27253852-G-A Benign (Jan 18, 2024)1270905
13-27253904-A-G Benign (Jul 14, 2018)1237877
13-27254247-G-A Hypotrichosis 12 Pathogenic (Jul 01, 2011)139638
13-27254929-G-GT Benign (Dec 04, 2020)1287865
13-27255173-G-A Benign (Jul 09, 2018)1235163
13-27255271-C-T Benign (Jan 18, 2024)1271809
13-27255347-C-A not specified Uncertain significance (Jan 02, 2024)3156049
13-27255962-A-G Benign (Feb 04, 2019)1233915
13-27256234-A-G not specified Uncertain significance (Dec 20, 2023)3156050
13-27256264-G-A not specified Uncertain significance (Jan 06, 2023)2460330
13-27256296-G-T Uncertain significance (Oct 07, 2022)2023111
13-27256307-A-G Likely benign (Nov 15, 2022)2858700
13-27256323-C-A Uncertain significance (Oct 05, 2023)2954969
13-27256337-A-G Benign (Jan 18, 2024)2122313
13-27256416-CT-C Benign (Oct 10, 2023)2964522
13-27256416-C-CT Likely benign (Sep 12, 2023)1988640
13-27256444-A-C Likely benign (Oct 10, 2023)2878327
13-27256507-C-G Likely benign (Jun 22, 2022)2182768
13-27256517-A-G not specified Uncertain significance (Sep 22, 2023)3156051
13-27256681-TG-T Benign (Jul 14, 2018)1227239

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL21protein_codingprotein_codingENST00000311549 55383
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8370.162123457011234580.00000405
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.534888.40.5430.000004561047
Missense in Polyphen25.74830.3479395
Synonymous-0.6183227.91.150.00000126289
Loss of Function2.69110.40.09666.91e-7110

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000009070.00000907
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of the large ribosomal subunit. {ECO:0000269|PubMed:23636399, ECO:0000269|PubMed:25901680, ECO:0000269|PubMed:25957688, ECO:0000305|PubMed:12962325}.;
Disease
DISEASE: Hypotrichosis 12 (HYPT12) [MIM:615885]: A form of hypotrichosis, a condition characterized by the presence of less than the normal amount of hair and abnormal hair follicles and shafts, which are thin and atrophic. The extent of scalp and body hair involvement can be very variable, within as well as between families. HYPT12 patients have normal scalp hair density at birth. Hair loss begins during the first 6 months of life and gradually progresses to nearly complete loss of scalp hair. The remaining hairs grow slowly and are thin, sparse, dry, and fragile. Body hair, axillary and pubic hair, eyebrows and eyelashes are also sparse or absent. {ECO:0000269|PubMed:21412954}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Ribosome - Homo sapiens (human);Cytoplasmic Ribosomal Proteins;SRP-dependent cotranslational protein targeting to membrane;Eukaryotic Translation Initiation;Eukaryotic Translation Termination;Translation;Selenocysteine synthesis;Metabolism of proteins;Metabolism of amino acids and derivatives;Metabolism of RNA;Formation of a pool of free 40S subunits;Metabolism;Nonsense-Mediated Decay (NMD);Selenoamino acid metabolism;Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC);Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC);L13a-mediated translational silencing of Ceruloplasmin expression;Peptide chain elongation;Eukaryotic Translation Elongation;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

pRec
0.206

Intolerance Scores

loftool
rvis_EVS
0.06
rvis_percentile_EVS
58

Haploinsufficiency Scores

pHI
0.304
hipred
Y
hipred_score
0.756
ghis
0.604

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.781

Gene Damage Prediction

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyLowLowLow
CancerLowLowLow

Mouse Genome Informatics

Gene name
Rpl21
Phenotype

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
Cellular component
endoplasmic reticulum;cytosol;membrane;cytosolic large ribosomal subunit
Molecular function
RNA binding;structural constituent of ribosome;protein binding