LARP4B

La ribonucleoprotein 4B, the group of La ribonucleoproteins

Basic information

Region (hg38): 10:806932-931821

Previous symbols: [ "KIAA0217", "LARP5" ]

Links

ENSG00000107929 ∙ NCBI:23185 ∙ OMIM:616513 ∙ HGNC:28987 ∙ Uniprot:Q92615 ∙ 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 LARP4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LARP4B 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					2	2
missense			31	5		36
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					1	1
non coding				2		2
Total	0	0	33	7	2

Variants in LARP4B

This is a list of pathogenic ClinVar variants found in the LARP4B region.

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

Position	Type	Phenotype	Significance	ClinVar
10-812942-G-C		not specified	Uncertain significance (Aug 17, 2022)
10-812990-G-A		not specified	Uncertain significance (Apr 17, 2023)
10-812993-G-T		not specified	Uncertain significance (Aug 30, 2021)
10-812996-C-T		not specified	Uncertain significance (Jan 26, 2023)
10-813063-G-A		not specified	Uncertain significance (Jul 06, 2021)
10-813064-G-T		not specified	Uncertain significance (May 04, 2022)
10-813083-G-A		not specified	Uncertain significance (May 30, 2024)
10-813124-C-G		not specified	Uncertain significance (Nov 17, 2022)
10-813136-T-C			Benign (Dec 26, 2018)
10-814782-G-A		not specified	Uncertain significance (Mar 30, 2024)
10-814786-T-C		not specified	Uncertain significance (Apr 27, 2024)
10-814826-C-G		not specified	Uncertain significance (Jan 04, 2022)
10-814850-A-T		not specified	Likely benign (Jan 17, 2024)
10-814971-A-T		not specified	Uncertain significance (Nov 08, 2022)
10-814982-G-A		not specified	Uncertain significance (Aug 10, 2021)
10-814983-T-C		not specified	Likely benign (May 31, 2024)
10-815028-C-A		not specified	Uncertain significance (Dec 20, 2023)
10-815030-A-G			Likely benign (Jan 01, 2023)
10-815050-G-A			Benign (Dec 26, 2018)
10-817747-A-G		not specified	Uncertain significance (Jun 17, 2024)
10-817757-A-G		not specified	Uncertain significance (Aug 13, 2021)
10-817784-T-G		not specified	Uncertain significance (Feb 12, 2024)
10-817843-C-T		not specified	Uncertain significance (Sep 07, 2022)
10-817868-T-C		not specified	Uncertain significance (Feb 17, 2022)
10-825064-C-T			Uncertain significance (Sep 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LARP4B	protein_coding	protein_coding	ENST00000316157	17	122081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000168	125740	0	5	125745	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	326	441	0.740	0.0000265	4774
Missense in Polyphen		76	138.11	0.5503		1575
Synonymous	-0.0259	182	182	1.00	0.0000126	1482
Loss of Function	5.55	2	39.8	0.0503	0.00000206	457

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	0.0000475	0.0000462
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stimulates mRNA translation. {ECO:0000269|PubMed:20573744}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.0360
• rvis_EVS: -1.06
• rvis_percentile_EVS: 7.48

Haploinsufficiency Scores

• pHI: 0.584
• hipred: Y
• hipred_score: 0.662
• ghis: 0.651

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.635

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Larp4b

Gene ontology

• Biological process: positive regulation of translation
• Cellular component: nucleolus;cytosol;cytoplasmic stress granule;membrane;polysomal ribosome
• Molecular function: RNA binding;protein binding