MRPS7

mitochondrial ribosomal protein S7, the group of Mitochondrial ribosomal proteins

Basic information

Region (hg38): 17:75261674-75266376

Links

ENSG00000125445 ∙ NCBI:51081 ∙ OMIM:611974 ∙ HGNC:14499 ∙ Uniprot:Q9Y2R9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• syndromic sensorineural deafness due to combined oxidative phosphorylation defect (Supportive), mode of inheritance: AR
• combined oxidative phosphorylation deficiency 34 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 34	AR	Audiologic/Otolaryngologic; Endocrine	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; Individuals have been described with endocrine abnormalities including adrenal failure, and awareness may allow early medical management	Audiologic/Otolaryngologic; Biochemical; Endocrine; Neurologic; Renal	25556185

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRPS7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS7 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				15		15
missense			29	5	1	35
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				7		7
non coding				14	15	29
Total	0	1	30	34	16

Variants in MRPS7

This is a list of pathogenic ClinVar variants found in the MRPS7 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-75261732-G-T			Benign (Jun 16, 2018)
17-75261851-G-A		not specified	Likely benign (Feb 08, 2017)
17-75261905-C-T		not specified • Combined oxidative phosphorylation deficiency 34	Benign (Jan 30, 2024)
17-75261911-C-G		not specified	Uncertain significance (Dec 11, 2023)
17-75261921-G-C			Uncertain significance (Aug 17, 2023)
17-75261925-G-A			Uncertain significance (Nov 16, 2023)
17-75261927-C-T		not specified	Likely benign (Nov 10, 2016)
17-75261947-C-T			Benign/Likely benign (Aug 01, 2024)
17-75261962-G-A			Uncertain significance (Dec 22, 2023)
17-75261966-T-C		not specified • MRPS7-related disorder	Likely benign (Jul 01, 2024)
17-75261980-C-T		not specified	Uncertain significance (Jun 29, 2022)
17-75261999-G-T			Likely benign (Apr 18, 2023)
17-75262001-AGCG-A			Benign (Aug 14, 2023)
17-75262003-CGG-C			Benign (Jun 23, 2018)
17-75262003-C-CG			Likely benign (Jan 23, 2020)
17-75262004-GGC-G		Combined oxidative phosphorylation deficiency 34	Benign (Sep 05, 2021)
17-75262005-G-C			Benign (Jun 14, 2018)
17-75262005-GC-G			Benign (Jul 17, 2018)
17-75262006-C-G		Combined oxidative phosphorylation deficiency 34	Benign (Sep 05, 2021)
17-75262006-C-T			Likely benign (Oct 29, 2019)
17-75262012-G-T			Benign (Jul 09, 2018)
17-75262120-G-T			Benign (Jul 09, 2018)
17-75262228-T-G			Benign (Jun 16, 2018)
17-75262398-C-T			Benign (Jun 23, 2018)
17-75262417-C-T			Likely benign (Jun 14, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS7	protein_coding	protein_coding	ENST00000245539	5	4700

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00126	0.865	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0787	150	147	1.02	0.00000863	1570
Missense in Polyphen		34	40.975	0.82977		522
Synonymous	-1.78	69	52.6	1.31	0.00000273	472
Loss of Function	1.30	6	10.5	0.569	4.53e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000243
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000716	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Combined oxidative phosphorylation deficiency 34 (COXPD34) [MIM:617872]: An autosomal recessive disorder caused by mitochondrial dysfunction and combined respiratory chain deficiencies of complexes I, III and IV. Clinical manifestations are variable and include congenital sensorineural deafness, lactic acidemia, and progressive hepatic and renal failure. {ECO:0000269|PubMed:25556185}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Ribosome - Homo sapiens (human);Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.240

Intolerance Scores

• loftool: 0.613
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.08

Haploinsufficiency Scores

• pHI: 0.0633
• hipred: Y
• hipred_score: 0.513
• ghis: 0.452

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.919

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrps7

Gene ontology

• Biological process: ribosomal small subunit assembly;translation;mitochondrial translation;mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: mitochondrial inner membrane;mitochondrial small ribosomal subunit
• Molecular function: RNA binding;mRNA binding;structural constituent of ribosome;rRNA binding