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RPS29

ribosomal protein S29, the group of S ribosomal proteins

Basic information

Region (hg38): 14:49570983-49599164

Links

ENSG00000213741NCBI:6235OMIM:603633HGNC:10419Uniprot:P62273AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Diamond-Blackfan anemia 13ADCardiovascular; Hematologic; OncologicSpecific 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 managementCardiovascular; Hematologic; Oncologic24829207

ClinVar

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

  • not provided (34 variants)
  • Diamond-Blackfan anemia 13 (3 variants)
  • Inborn genetic diseases (2 variants)
  • not specified (1 variants)
  • RPS29-related condition (1 variants)

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
clinvar
8
clinvar
9
missense
2
clinvar
10
clinvar
1
clinvar
13
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
2
3
1
7
non coding
7
clinvar
2
clinvar
9
Total 0 2 11 16 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)1248443
14-49577821-T-C RPS29-related disorder Likely benign (Jun 05, 2023)3054139
14-49583662-A-C RPS29-related disorder Likely benign (Jul 05, 2022)3053910
14-49583678-GA-G Diamond-Blackfan anemia 13 Benign/Likely benign (Nov 21, 2023)1293204
14-49583678-G-GA Benign (Oct 05, 2023)1248271
14-49583688-A-C Likely benign (May 25, 2021)1561313
14-49583692-A-G Likely benign (Sep 19, 2023)2423256
14-49583693-G-A Likely benign (Dec 02, 2023)2424357
14-49583732-C-T Benign (Jun 05, 2019)1223950
14-49585933-C-G Likely benign (Jun 26, 2021)1554931
14-49585934-G-A Uncertain significance (Feb 28, 2021)1513944
14-49585942-A-C Likely benign (Jul 19, 2023)2897056
14-49585943-C-A Likely benign (Nov 23, 2022)3018785
14-49585946-C-A Uncertain significance (Sep 08, 2020)1020787
14-49585947-T-C Uncertain significance (Jun 20, 2022)1434119
14-49585955-T-C Inborn genetic diseases Uncertain significance (Feb 27, 2024)1440649
14-49585956-G-A Likely benign (Jan 09, 2024)2885455
14-49585963-A-G Diamond-Blackfan anemia 13 Likely pathogenic (Jun 26, 2019)140739
14-49585972-G-A Uncertain significance (Sep 08, 2023)2866763
14-49585973-C-A Inborn genetic diseases Uncertain significance (Nov 12, 2021)2260558
14-49585986-A-G Likely benign (Dec 11, 2023)1642811
14-49585990-T-C Inborn genetic diseases Uncertain significance (Dec 11, 2023)3156188
14-49585995-G-A Likely benign (Apr 25, 2021)1609740
14-49586010-A-G Likely benign (May 02, 2023)2082765
14-49586021-T-A Diamond-Blackfan anemia 13 Pathogenic (Jul 03, 2014)140738

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS29protein_codingprotein_codingENST00000396020 322019
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.2910.634102073011020740.00000490
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.022138.90.5400.00000176435
Missense in Polyphen520.3640.24553200
Synonymous-0.1261514.41.046.49e-7116
Loss of Function1.3513.870.2581.64e-741

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00003520.0000352
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

loftool
rvis_EVS
0.04
rvis_percentile_EVS
56.25

Haploinsufficiency Scores

pHI
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

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyLowLowLow
CancerLowLowLow

Mouse Genome Informatics

Gene name
Rps29
Phenotype

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