RPS7

ribosomal protein S7, the group of S ribosomal proteins

Basic information

Region (hg38): 2:3575259-3580920

Links

ENSG00000171863 ∙ NCBI:6201 ∙ OMIM:603658 ∙ HGNC:10440 ∙ Uniprot:P62081 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diamond-Blackfan anemia 8	AD	Hematologic; Oncologic	Specific 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 management	Craniofacial; Hematologic; Oncologic	16317735; 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	29	2	33
missense			37			37
nonsense						0
start loss						0
frameshift		1				1
inframe indel			1			1
splice donor/acceptor (+/-2bp)	2					2
splice region			11	6	1	18
non coding	2	1	10	24	21	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)
2-3575265-G-A		Diamond-Blackfan anemia	Likely benign (Jun 14, 2016)
2-3575283-C-T		Diamond-Blackfan anemia 8	Uncertain significance (Jan 12, 2018)
2-3575322-G-T		Diamond-Blackfan anemia 8 • not specified	Benign (Jan 12, 2018)
2-3575325-C-T		Diamond-Blackfan anemia 8	Uncertain significance (Jan 12, 2018)
2-3575333-A-C		Diamond-Blackfan anemia 8	Benign (Jan 13, 2018)
2-3575342-C-T		Diamond-Blackfan anemia 8	Uncertain significance (Jan 12, 2018)
2-3575346-G-A		Diamond-Blackfan anemia 8	Uncertain significance (Jan 12, 2018)
2-3575349-AG-A		Diamond-Blackfan anemia 8	Uncertain significance (May 23, 2023)
2-3575350-G-C		Diamond-Blackfan anemia 8	Uncertain significance (Jun 23, 2023)
2-3575351-G-A		Diamond-Blackfan anemia 8	Likely pathogenic (May 02, 2023)
2-3575351-G-C			Uncertain significance (Mar 13, 2017)
2-3575351-G-T		Diamond-Blackfan anemia 8	Pathogenic (Jul 21, 2023)
2-3575352-T-A		Diamond-Blackfan anemia 8	Pathogenic (Dec 09, 2023)
2-3575363-C-T		Diamond-Blackfan anemia 8	Benign/Likely benign (Sep 07, 2021)
2-3575597-C-T		Diamond-Blackfan anemia 8	Uncertain significance (Jan 13, 2018)
2-3575607-G-A		Diamond-Blackfan anemia 8	Uncertain significance (Apr 11, 2019)
2-3575620-C-T			Uncertain significance (Jan 26, 2017)
2-3575623-G-A		Diamond-Blackfan anemia 8	Uncertain significance (Jul 29, 2021)
2-3575633-C-A		Diamond-Blackfan anemia 8	Likely benign (Feb 20, 2022)
2-3575633-C-T		Diamond-Blackfan anemia 8	Likely benign (Dec 23, 2021)
2-3575640-C-T		Diamond-Blackfan anemia 8	Uncertain significance (Aug 16, 2022)
2-3575643-A-C		Diamond-Blackfan anemia 8	Uncertain significance (Nov 08, 2019)
2-3575644-A-G		Diamond-Blackfan anemia 8	Uncertain significance (Apr 24, 2023)
2-3575648-C-T		Diamond-Blackfan anemia • Diamond-Blackfan anemia 8	Conflicting classifications of pathogenicity (Aug 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS7	protein_coding	protein_coding	ENST00000304921	6	5715

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.954	0.0455	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	63	111	0.566	0.00000700	1278
Missense in Polyphen		3	12.589	0.2383		226
Synonymous	-1.97	61	44.3	1.38	0.00000267	375
Loss of Function	2.88	0	9.69	0.00	4.83e-7	115

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

• 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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