RPL31

ribosomal protein L31, the group of L ribosomal proteins

Basic information

Region (hg38): 2:101002228-101024032

Links

ENSG00000071082 ∙ NCBI:6160 ∙ OMIM:617415 ∙ HGNC:10334 ∙ Uniprot:P62899 ∙ 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 RPL31 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL31 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				7	1	8
missense			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			1	2		3
non coding			1	7	8	16
Total	0	0	14	15	9

Variants in RPL31

This is a list of pathogenic ClinVar variants found in the RPL31 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-101002740-C-G			Likely benign (Jan 21, 2024)
2-101002740-C-T			Likely benign (Sep 05, 2022)
2-101002749-C-T			Benign (Oct 27, 2023)
2-101002753-A-G			Uncertain significance (Sep 03, 2023)
2-101002780-A-G			Uncertain significance (Oct 11, 2023)
2-101002804-G-A		not specified	Uncertain significance (Jan 03, 2024)
2-101002815-A-G			Likely benign (May 03, 2022)
2-101002817-C-T			Likely benign (Nov 25, 2023)
2-101002821-C-G			Benign (Jan 31, 2024)
2-101002825-C-T			Likely benign (Sep 27, 2022)
2-101002859-T-C			Benign (May 14, 2021)
2-101002870-G-A			Benign (May 24, 2021)
2-101002915-C-T			Benign (May 17, 2021)
2-101004140-C-T			Likely benign (Sep 15, 2023)
2-101004144-T-C			Likely benign (Sep 24, 2023)
2-101004153-C-T			Likely benign (Jul 03, 2023)
2-101004181-G-A			Uncertain significance (Sep 07, 2022)
2-101004187-T-G			Uncertain significance (Nov 22, 2023)
2-101004190-A-G		not specified	Uncertain significance (Apr 17, 2023)
2-101004198-C-T		not specified	Uncertain significance (Jun 29, 2023)
2-101004199-G-A			Uncertain significance (Sep 22, 2023)
2-101004206-T-A		not specified	Uncertain significance (Oct 10, 2023)
2-101004213-AAGG-A			Uncertain significance (May 25, 2022)
2-101004238-G-A			Uncertain significance (Jul 24, 2023)
2-101004242-T-C			Likely benign (Mar 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL31	protein_coding	protein_coding	ENST00000409028	4	22318

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.850	0.148	122014	0	4	122018	0.0000164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	39	80.4	0.485	0.00000487	820
Missense in Polyphen		4	4.3461	0.92037		68
Synonymous	-0.198	28	26.7	1.05	0.00000123	261
Loss of Function	2.31	0	6.22	0.00	3.53e-7	71

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)	0.0000362	0.0000362
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Ribosome - Homo sapiens (human);Cytoplasmic Ribosomal Proteins;SRP-dependent cotranslational protein targeting to membrane;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);L13a-mediated translational silencing of Ceruloplasmin expression;Peptide chain elongation;Eukaryotic Translation Elongation;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

• pRec: 0.202

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.72

Haploinsufficiency Scores

• pHI: 0.233
• hipred: Y
• hipred_score: 0.669
• ghis: 0.413

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpl31
• Phenotype: endocrine/exocrine gland phenotype; reproductive system 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); limbs/digits/tail phenotype

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
• Cellular component: cytosol;focal adhesion;membrane;cytosolic large ribosomal subunit;polysomal ribosome;extracellular exosome
• Molecular function: RNA binding;structural constituent of ribosome;protein binding