RPL21

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

Basic information

Region (hg38): 13:27251362-27259609

Links

ENSG00000122026 ∙ NCBI:6144 ∙ OMIM:603636 ∙ HGNC:10313 ∙ Uniprot:P46778 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypotrichosis 12	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic	19751230; 21412954

ClinVar

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

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				4	1	5
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		1	2
non coding				1	7	8
Total	0	0	6	5	8

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)
13-27253839-A-G			Likely benign (Jan 24, 2023)
13-27253842-T-C			Uncertain significance (Aug 11, 2023)
13-27253852-G-A			Benign (Jan 18, 2024)
13-27253904-A-G			Benign (Jul 14, 2018)
13-27254247-G-A		Hypotrichosis 12	Pathogenic (Jul 01, 2011)
13-27254929-G-GT			Benign (Dec 04, 2020)
13-27255173-G-A			Benign (Jul 09, 2018)
13-27255271-C-T			Benign (Jan 18, 2024)
13-27255347-C-A		not specified	Uncertain significance (Jan 02, 2024)
13-27255962-A-G			Benign (Feb 04, 2019)
13-27256234-A-G		not specified	Uncertain significance (Dec 20, 2023)
13-27256264-G-A		not specified	Uncertain significance (Jan 06, 2023)
13-27256296-G-T			Uncertain significance (Oct 07, 2022)
13-27256307-A-G			Likely benign (Nov 15, 2022)
13-27256323-C-A			Uncertain significance (Oct 05, 2023)
13-27256337-A-G			Benign (Jan 18, 2024)
13-27256416-CT-C			Benign (Oct 10, 2023)
13-27256416-C-CT			Likely benign (Sep 12, 2023)
13-27256444-A-C			Likely benign (Oct 10, 2023)
13-27256507-C-G			Likely benign (Jun 22, 2022)
13-27256517-A-G		not specified	Uncertain significance (Sep 22, 2023)
13-27256681-TG-T			Benign (Jul 14, 2018)
13-27256811-A-C			Benign (May 19, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL21	protein_coding	protein_coding	ENST00000311549	5	5383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.837	0.162	123457	0	1	123458	0.00000405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	48	88.4	0.543	0.00000456	1047
Missense in Polyphen		2	5.7483	0.34793		95
Synonymous	-0.618	32	27.9	1.15	0.00000126	289
Loss of Function	2.69	1	10.4	0.0966	6.91e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000907	0.00000907
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

• 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_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Rpl21

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