RPS29

ribosomal protein S29, the group of S ribosomal proteins

Basic information

Region (hg38): 14:49570983-49599164

Links

ENSG00000213741 ∙ NCBI:6235 ∙ OMIM:603633 ∙ HGNC:10419 ∙ Uniprot:P62273 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Diamond-Blackfan anemia 13 (Moderate), mode of inheritance: AD
• Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
• Diamond-Blackfan anemia 13 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diamond-Blackfan anemia 13	AD	Cardiovascular; Hematologic; Oncologic	Specific treatment of anemia (eg, steroids, regular transfusions) can be effective; Surveillance for and early treatment of malignancy may allow early detection and management; Individuals with DBA may manifest a variety of congenital malformations (eg, cardiac anomalies), and awareness may allow prompt detection and management	Cardiovascular; Hematologic; Oncologic	24829207

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS29 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS29 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	11		12
missense		2	14	3		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region		1	2	4	1	8
non coding			1	10	2	13
Total	0	2	16	24	2

Variants in RPS29

This is a list of pathogenic ClinVar variants found in the RPS29 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-49577674-T-C			Benign (Jun 29, 2018)
14-49577821-T-C		RPS29-related disorder	Likely benign (Jun 05, 2023)
14-49583662-A-C		RPS29-related disorder	Likely benign (Jul 05, 2022)
14-49583678-GA-G		Diamond-Blackfan anemia 13	Benign/Likely benign (Nov 21, 2023)
14-49583678-G-GA			Benign (Oct 05, 2023)
14-49583688-A-C			Likely benign (May 25, 2021)
14-49583692-A-G			Likely benign (Sep 19, 2023)
14-49583693-G-A			Likely benign (Dec 02, 2023)
14-49583732-C-T			Benign (Jun 05, 2019)
14-49585933-C-G			Likely benign (Jun 26, 2021)
14-49585934-G-A			Uncertain significance (Feb 28, 2021)
14-49585942-A-C			Likely benign (Jul 19, 2023)
14-49585943-C-A			Likely benign (Nov 23, 2022)
14-49585946-C-A			Uncertain significance (Sep 08, 2020)
14-49585947-T-C			Uncertain significance (Jun 20, 2022)
14-49585955-T-C		Inborn genetic diseases	Uncertain significance (Feb 27, 2024)
14-49585956-G-A			Likely benign (Jan 09, 2024)
14-49585963-A-G		Diamond-Blackfan anemia 13	Likely pathogenic (Jun 26, 2019)
14-49585972-G-A			Uncertain significance (Sep 08, 2023)
14-49585973-C-A		Inborn genetic diseases	Uncertain significance (Nov 12, 2021)
14-49585986-A-G			Likely benign (Dec 11, 2023)
14-49585990-T-C		Inborn genetic diseases	Uncertain significance (Dec 11, 2023)
14-49585995-G-A			Likely benign (Apr 25, 2021)
14-49586010-A-G			Likely benign (May 02, 2023)
14-49586021-T-A		Diamond-Blackfan anemia 13	Pathogenic (Jul 03, 2014)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS29	protein_coding	protein_coding	ENST00000396020	3	22019

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.291	0.634	102073	0	1	102074	0.00000490

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	21	38.9	0.540	0.00000176	435
Missense in Polyphen		5	20.364	0.24553		200
Synonymous	-0.126	15	14.4	1.04	6.49e-7	116
Loss of Function	1.35	1	3.87	0.258	1.64e-7	41

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000352	0.0000352
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Diamond-Blackfan anemia 13 (DBA13) [MIM:615909]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of malignancy. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. {ECO:0000269|PubMed:24829207}. 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;Formation of the ternary complex, and subsequently, the 43S complex;Translation initiation complex formation;Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S;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);Ribosomal scanning and start codon recognition;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: 0.0852

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.801
• ghis: 0.587

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rps29

Zebrafish Information Network

• Gene name: rps29
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
• Cellular component: nucleoplasm;cytosol;focal adhesion;small ribosomal subunit;cytosolic small ribosomal subunit;polysomal ribosome;extracellular exosome;cytoplasmic side of rough endoplasmic reticulum membrane
• Molecular function: structural constituent of ribosome;zinc ion binding