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RPS7

ribosomal protein S7, the group of S ribosomal proteins

Basic information

Region (hg38): 2:3575259-3580920

Links

ENSG00000171863NCBI:6201OMIM:603658HGNC:10440Uniprot:P62081AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Diamond-Blackfan anemia 8 (Strong), mode of inheritance: AD
  • Diamond-Blackfan anemia (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Diamond-Blackfan anemia 8ADHematologic; OncologicSpecific treatment of anemia (eg, steroids, regular transfusions) can be effective; surveillance for and early treatment of malignancy may be beneficial; Individuals with DBA may manifest a variety of congenital malformations, and awareness may allow prompt detection and managementCraniofacial; Hematologic; Oncologic16317735; 19061985; 20301769; 23718193; 23812780

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS7 gene.

  • Diamond-Blackfan anemia 8 (123 variants)
  • not provided (28 variants)
  • Diamond-Blackfan anemia (13 variants)
  • not specified (8 variants)
  • RPS7-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS7 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
2
clinvar
29
clinvar
2
clinvar
33
missense
37
clinvar
37
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
2
clinvar
2
splice region
?
11
6
1
18
non coding
?
2
clinvar
1
clinvar
10
clinvar
24
clinvar
21
clinvar
58
Total 4 2 50 53 23

Variants in RPS7

This is a list of pathogenic ClinVar variants found in the RPS7 region.

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

Position Type Phenotype Significance ClinVar
2-3575260-C-T Diamond-Blackfan anemia Likely benign (Jun 14, 2016)369341
2-3575265-G-A Diamond-Blackfan anemia Likely benign (Jun 14, 2016)335893
2-3575283-C-T Diamond-Blackfan anemia 8 Uncertain significance (Jan 12, 2018)335894
2-3575322-G-T Diamond-Blackfan anemia 8 • not specified Benign (Jan 12, 2018)335895
2-3575325-C-T Diamond-Blackfan anemia 8 Uncertain significance (Jan 12, 2018)335896
2-3575333-A-C Diamond-Blackfan anemia 8 Benign (Jan 13, 2018)335897
2-3575342-C-T Diamond-Blackfan anemia 8 Uncertain significance (Jan 12, 2018)335898
2-3575346-G-A Diamond-Blackfan anemia 8 Uncertain significance (Jan 12, 2018)335899
2-3575349-AG-A Diamond-Blackfan anemia 8 Uncertain significance (May 23, 2023)2689887
2-3575350-G-C Diamond-Blackfan anemia 8 Uncertain significance (Jun 23, 2023)2689888
2-3575351-G-A Diamond-Blackfan anemia 8 Likely pathogenic (May 02, 2023)975849
2-3575351-G-C Uncertain significance (Mar 13, 2017)424204
2-3575351-G-T Diamond-Blackfan anemia 8 Pathogenic (Jul 21, 2023)2697321
2-3575352-T-A Diamond-Blackfan anemia 8 Pathogenic (Dec 09, 2023)2761151
2-3575363-C-T Diamond-Blackfan anemia 8 Benign/Likely benign (Sep 07, 2021)335900
2-3575597-C-T Diamond-Blackfan anemia 8 Uncertain significance (Jan 13, 2018)335901
2-3575607-G-A Diamond-Blackfan anemia 8 Uncertain significance (Apr 11, 2019)1028444
2-3575620-C-T Uncertain significance (Jan 26, 2017)392905
2-3575623-G-A Diamond-Blackfan anemia 8 Uncertain significance (Jul 29, 2021)1485908
2-3575633-C-A Diamond-Blackfan anemia 8 Likely benign (Feb 20, 2022)1960904
2-3575633-C-T Diamond-Blackfan anemia 8 Likely benign (Dec 23, 2021)1936094
2-3575640-C-T Diamond-Blackfan anemia 8 Uncertain significance (Aug 16, 2022)1368521
2-3575643-A-C Diamond-Blackfan anemia 8 Uncertain significance (Nov 08, 2019)955608
2-3575644-A-G Diamond-Blackfan anemia 8 Uncertain significance (Apr 24, 2023)998359
2-3575648-C-T Diamond-Blackfan anemia • Diamond-Blackfan anemia 8 Conflicting classifications of pathogenicity (Sep 14, 2022)335902

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS7protein_codingprotein_codingENST00000304921 65715
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9540.045500000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.63631110.5660.000007001278
Missense in Polyphen312.5890.2383226
Synonymous-1.976144.31.380.00000267375
Loss of Function2.8809.690.004.83e-7115

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)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Required for rRNA maturation. {ECO:0000269|PubMed:19061985}.;
Disease
DISEASE: Diamond-Blackfan anemia 8 (DBA8) [MIM:612563]: 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:19061985}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Ribosome - Homo sapiens (human);Cytoplasmic Ribosomal Proteins;rRNA processing;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;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

pRec
0.292

Intolerance Scores

loftool
rvis_EVS
-0.1
rvis_percentile_EVS
46.2

Haploinsufficiency Scores

pHI
0.969
hipred
Y
hipred_score
0.756
ghis
0.696

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
N
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.980

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rps7
Phenotype
growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; limbs/digits/tail phenotype; vision/eye phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); pigmentation phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Zebrafish Information Network

Gene name
rps7
Affected structure
nucleate erythrocyte
Phenotype tag
abnormal
Phenotype quality
decreased amount

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;neural tube closure;rRNA processing;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;positive regulation of gene expression;cell differentiation;ribosomal small subunit biogenesis;protein stabilization;positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator;negative regulation of ubiquitin protein ligase activity;negative regulation of ubiquitin-dependent protein catabolic process
Cellular component
nucleus;nucleoplasm;nucleolus;centrosome;cytosol;ribosome;focal adhesion;membrane;cytosolic small ribosomal subunit;small-subunit processome;protein-containing complex;synapse;ribonucleoprotein complex
Molecular function
RNA binding;mRNA 3'-UTR binding;structural constituent of ribosome;protein binding;poly(U) RNA binding;protein kinase binding;mRNA 5'-UTR binding;ubiquitin ligase inhibitor activity