MRPS30

mitochondrial ribosomal protein S30, the group of Small subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 5:44808947-44820428

Previous symbols: [ "PDCD9" ]

Links

ENSG00000112996 ∙ NCBI:10884 ∙ OMIM:611991 ∙ HGNC:8769 ∙ Uniprot:Q9NP92 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRPS30 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS30 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						0
missense			39			39
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	1	0

Variants in MRPS30

This is a list of pathogenic ClinVar variants found in the MRPS30 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-44808969-G-C		not specified	Uncertain significance (Aug 21, 2023)
5-44808970-C-T		not specified	Uncertain significance (Sep 17, 2021)
5-44808976-G-A		not specified	Uncertain significance (Aug 09, 2021)
5-44809117-C-T		not specified	Uncertain significance (Jan 11, 2023)
5-44809152-G-A		not specified	Uncertain significance (May 18, 2023)
5-44809164-G-A		not specified	Uncertain significance (Aug 20, 2024)
5-44809165-C-A		not specified	Uncertain significance (Aug 20, 2024)
5-44809180-C-G		not specified	Uncertain significance (Jul 26, 2024)
5-44809185-T-C		not specified	Uncertain significance (Sep 27, 2024)
5-44809200-C-A		not specified	Uncertain significance (Jan 21, 2025)
5-44809224-T-G		not specified	Uncertain significance (Mar 18, 2024)
5-44809266-G-A		not specified	Uncertain significance (Jun 22, 2024)
5-44809273-G-A		not specified	Uncertain significance (May 26, 2023)
5-44809290-A-T		not specified	Uncertain significance (Dec 25, 2024)
5-44809296-A-G		not specified	Uncertain significance (Dec 14, 2023)
5-44809331-G-GGAGCCC			Likely benign (Feb 01, 2024)
5-44809338-G-A		not specified	Uncertain significance (Aug 16, 2021)
5-44809392-G-A		not specified	Uncertain significance (Jun 28, 2024)
5-44809399-C-T		not specified	Uncertain significance (Aug 20, 2024)
5-44809423-A-G		not specified	Uncertain significance (Aug 28, 2024)
5-44809446-C-G		not specified	Uncertain significance (Dec 03, 2021)
5-44809491-C-G		not specified	Uncertain significance (Oct 26, 2024)
5-44811042-G-T		not specified	Uncertain significance (Apr 07, 2022)
5-44811081-G-A			not provided (-)
5-44811114-A-C		not specified	Uncertain significance (Mar 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS30	protein_coding	protein_coding	ENST00000507110	5	11504

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.59e-8	0.626	125644	0	104	125748	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.934	293	251	1.17	0.0000122	2813
Missense in Polyphen		97	96.172	1.0086		1129
Synonymous	-2.74	138	103	1.34	0.00000484	892
Loss of Function	1.20	15	20.9	0.716	0.00000124	201

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000571	0.000570
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000878	0.000878
European (Non-Finnish)	0.000453	0.000448
Middle Eastern	0.000163	0.000163
South Asian	0.000468	0.000457
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.800
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.71

Haploinsufficiency Scores

• pHI: 0.354
• hipred: N
• hipred_score: 0.150
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.877

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrps30

Gene ontology

• Biological process: apoptotic process;mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: mitochondrion;mitochondrial inner membrane;mitochondrial large ribosomal subunit
• Molecular function: RNA binding;structural constituent of ribosome