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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL31 gene.

• not provided (29 variants)
• Inborn genetic diseases (10 variants)
• not specified (1 variants)

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	1	6
missense			4	1		5
nonsense						0
start loss						0
frameshift			1			1
inframe indel			1			1
splice variant				1		1
non coding			10	1	14	25
Total	0	0	16	8	15

Variants in RPL31

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

Position	Type	Phenotype	Significance	ClinVar
2-101002740-C-G			Likely benign (Oct 31, 2022)
2-101002740-C-T			Likely benign (Sep 05, 2022)
2-101002749-C-T			Benign (Oct 16, 2022)
2-101002804-G-A			Uncertain significance (Sep 27, 2022)
2-101002815-A-G			Likely benign (May 03, 2022)
2-101002821-C-G			Benign (Nov 03, 2022)
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)
2-101004181-G-A			Uncertain significance (Sep 07, 2022)
2-101004190-A-G		Inborn genetic diseases	Uncertain significance (May 04, 2022)
2-101004198-C-T		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
2-101004213-AAGG-A			Uncertain significance (May 25, 2022)
2-101004263-T-C			Likely benign (Apr 12, 2022)
2-101004304-C-G			Benign (May 18, 2021)
2-101005769-C-T			Benign (May 14, 2021)
2-101005947-T-A			Uncertain significance (Aug 24, 2022)
2-101005977-C-T		not specified	Likely benign (Oct 26, 2022)
2-101005985-G-A			Uncertain significance (Aug 10, 2022)
2-101006029-C-T			Likely benign (Jul 19, 2022)
2-101006060-C-A			Likely benign (Oct 17, 2022)
2-101006165-C-A			Benign (May 24, 2021)
2-101006266-C-T			Benign (May 14, 2021)
2-101007861-C-T		Inborn genetic diseases	Uncertain significance (Jan 10, 2022)

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