LARP1B

La ribonucleoprotein 1B, the group of La ribonucleoproteins

Basic information

Region (hg38): 4:128061286-128222931

Previous symbols: [ "LARP2" ]

Links

ENSG00000138709 ∙ NCBI:55132 ∙ ∙ HGNC:24704 ∙ Uniprot:Q659C4 ∙ 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 LARP1B gene.

• not_specified (121 variants)
• Prostate_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LARP1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018078.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			116	6		122
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	116	6	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LARP1B	protein_coding	protein_coding	ENST00000326639	18	161664

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.53e-11	1.00	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.521	437	469	0.932	0.0000237	6013
Missense in Polyphen		101	125.97	0.80179		1657
Synonymous	1.04	135	151	0.892	0.00000713	1662
Loss of Function	3.41	27	54.0	0.500	0.00000336	623

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000501	0.000481
Ashkenazi Jewish	0.00	0.00
East Asian	0.000498	0.000489
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000179	0.000149
Middle Eastern	0.000498	0.000489
South Asian	0.000209	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.958
• rvis_EVS: 0.76
• rvis_percentile_EVS: 86.83

Haploinsufficiency Scores

• pHI: 0.653
• hipred: N
• hipred_score: 0.306
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.189

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Larp1b

Gene ontology

• Cellular component: nucleus
• Molecular function: RNA binding;protein binding