LARP1

La ribonucleoprotein 1, translational regulator, the group of MicroRNA protein coding host genes|La ribonucleoproteins

Basic information

Region (hg38): 5:154682985-154817605

Links

ENSG00000155506 ∙ NCBI:23367 ∙ OMIM:612059 ∙ HGNC:29531 ∙ Uniprot:Q6PKG0 ∙ 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 LARP1 gene.

• Inborn genetic diseases (25 variants)
• not provided (3 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LARP1 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				1	1	2
missense			25	1	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	2

Variants in LARP1

This is a list of pathogenic ClinVar variants found in the LARP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-154713047-T-G		not specified	Uncertain significance (Dec 15, 2023)
5-154790364-C-G		not specified	Uncertain significance (Jul 12, 2023)
5-154792746-A-T		not specified	Uncertain significance (Jul 12, 2023)
5-154793616-C-T		not specified	Uncertain significance (Mar 11, 2022)
5-154793666-C-T		not specified	Uncertain significance (Jan 08, 2024)
5-154793721-A-G		not specified	Uncertain significance (Dec 01, 2022)
5-154793826-G-A			Likely benign (Jul 27, 2018)
5-154793832-C-A		not specified	Uncertain significance (Sep 14, 2021)
5-154793852-A-G			Likely benign (Oct 01, 2022)
5-154793899-C-T		not specified	Uncertain significance (Apr 18, 2023)
5-154793910-A-T		not specified	Uncertain significance (Jul 05, 2023)
5-154793941-T-C		not specified	Uncertain significance (Jul 12, 2023)
5-154793949-C-T		not specified	Uncertain significance (Jul 12, 2022)
5-154794157-C-T		not specified	Uncertain significance (Mar 21, 2022)
5-154794225-G-T		not specified	Uncertain significance (Jul 20, 2022)
5-154799675-A-G		not specified	Uncertain significance (Mar 20, 2023)
5-154799896-G-T		not specified	Uncertain significance (Sep 26, 2023)
5-154799897-C-A		not specified	Uncertain significance (Jun 23, 2023)
5-154799897-C-T		not specified	Uncertain significance (Dec 18, 2023)
5-154802188-A-G		not specified	Uncertain significance (Dec 15, 2022)
5-154802245-A-G		not specified	Uncertain significance (Jun 29, 2023)
5-154802268-G-C		not specified	Uncertain significance (Feb 06, 2023)
5-154803304-C-A		not specified	Uncertain significance (Jun 02, 2023)
5-154803578-C-T		not specified	Uncertain significance (May 30, 2023)
5-154805975-A-C		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LARP1	protein_coding	protein_coding	ENST00000336314	19	104706

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000123	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.07	406	621	0.654	0.0000385	6684
Missense in Polyphen		166	297.58	0.55783		2987
Synonymous	0.911	207	224	0.923	0.0000126	1996
Loss of Function	6.41	4	55.6	0.0720	0.00000327	595

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein that promotes translation of specific classes of mRNAs downstream of the mTORC1 complex (PubMed:24532714, PubMed:25940091). Associates with the mRNA 5'cap in an MTOR-dependent manner and associates with mRNAs containing a 5' terminal oligopyrimidine (5'TOP) motif, which is present in mRNAs encoding for ribosomal proteins and several components of the translation machinery (PubMed:24532714, PubMed:25940091, PubMed:26206669). Associates with actively translating ribosomes via interaction with PABPC1/PABP and stimulates translation of mRNAs containing a 5'TOP, thereby regulating cell growth and proliferation (PubMed:20430826, PubMed:25940091). Positively regulates the replication of dengue virus (DENV) (PubMed:26735137). {ECO:0000269|PubMed:20430826, ECO:0000269|PubMed:24532714, ECO:0000269|PubMed:26206669, ECO:0000269|PubMed:26735137}.

Recessive Scores

• pRec: 0.0905

Intolerance Scores

• loftool: 0.573
• rvis_EVS: -1.35
• rvis_percentile_EVS: 4.6

Haploinsufficiency Scores

• pHI: 0.276
• hipred: Y
• hipred_score: 0.728
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.905

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Larp1

Gene ontology

• Biological process: translational initiation;cell population proliferation;positive regulation of macroautophagy;negative regulation of translation;TOR signaling;TORC1 signaling;positive regulation of viral genome replication;positive regulation of translation;mRNA stabilization;cellular response to rapamycin;response to amino acid starvation
• Cellular component: cytoplasm;polysome;cytoplasmic stress granule;membrane;TORC1 complex
• Molecular function: RNA cap binding;RNA binding;mRNA 3'-UTR binding;protein binding;eukaryotic initiation factor 4E binding;translation activator activity;translation initiation factor binding;cadherin binding;mRNA 5'-UTR binding