MRPS31

mitochondrial ribosomal protein S31, the group of Small subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 13:40729128-40771190

Links

ENSG00000102738 ∙ NCBI:10240 ∙ OMIM:611992 ∙ HGNC:16632 ∙ Uniprot:Q92665 ∙ 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 MRPS31 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS31 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			30	2		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	0

Variants in MRPS31

This is a list of pathogenic ClinVar variants found in the MRPS31 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-40729380-A-G		not specified	Uncertain significance (May 24, 2024)
13-40729389-T-C		not specified	Uncertain significance (Nov 03, 2022)
13-40729438-C-A		not specified	Uncertain significance (Feb 16, 2023)
13-40729466-C-T		not specified	Uncertain significance (Oct 04, 2022)
13-40729508-A-G		not specified	Uncertain significance (Dec 13, 2022)
13-40729521-T-A		not specified	Uncertain significance (Mar 25, 2024)
13-40729579-T-A		not specified	Uncertain significance (Mar 29, 2024)
13-40729586-C-T		not specified	Uncertain significance (Jan 20, 2023)
13-40729587-C-T		not specified	Uncertain significance (Nov 29, 2023)
13-40749146-T-C		not specified	Uncertain significance (Dec 21, 2023)
13-40749262-C-G		not specified	Uncertain significance (Apr 11, 2023)
13-40749272-G-A		not specified	Uncertain significance (Jul 21, 2021)
13-40754025-C-T		not specified	Uncertain significance (Nov 14, 2023)
13-40754063-T-A		not specified	Uncertain significance (Jun 17, 2024)
13-40754069-C-G		not specified	Uncertain significance (Mar 22, 2023)
13-40756878-T-G		not specified	Uncertain significance (Jan 08, 2024)
13-40756907-G-T		not specified	Uncertain significance (Aug 17, 2022)
13-40756975-G-C		not specified	Uncertain significance (May 26, 2022)
13-40758985-A-G		not specified	Uncertain significance (Sep 26, 2023)
13-40759086-T-G		not specified	Uncertain significance (Oct 30, 2023)
13-40766776-C-T		not specified	Likely benign (Oct 26, 2021)
13-40766781-C-G		not specified	Uncertain significance (Apr 24, 2023)
13-40766856-T-A		not specified	Uncertain significance (Apr 08, 2022)
13-40766900-T-C		not specified	Uncertain significance (Nov 15, 2021)
13-40766995-C-T		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS31	protein_coding	protein_coding	ENST00000323563	7	41878

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000538	0.972	125695	0	35	125730	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.102	200	204	0.980	0.00000953	2591
Missense in Polyphen		46	55.767	0.82486		827
Synonymous	0.278	69	72.0	0.958	0.00000328	736
Loss of Function	1.98	10	19.4	0.515	0.00000113	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000198	0.000195
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000583	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000236	0.000229
Middle Eastern	0.0000583	0.0000544
South Asian	0.0000788	0.0000653
Other	0.000354	0.000326

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0684

Intolerance Scores

• loftool: 0.872
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.172
• hipred: N
• hipred_score: 0.123
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.938

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrps31

Gene ontology

• Biological process: mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: nucleolus;mitochondrion;mitochondrial inner membrane;mitochondrial small ribosomal subunit
• Molecular function: RNA binding;structural constituent of ribosome;protein binding;protein domain specific binding