LARP4

La ribonucleoprotein 4, the group of La ribonucleoproteins

Basic information

Region (hg38): 12:50392383-50480004

Links

ENSG00000161813 ∙ NCBI:113251 ∙ OMIM:618657 ∙ HGNC:24320 ∙ Uniprot:Q71RC2 ∙ 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 LARP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LARP4 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						0
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in LARP4

This is a list of pathogenic ClinVar variants found in the LARP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-50396303-C-T		not specified	Uncertain significance (Mar 15, 2024)
12-50396324-A-G		not specified	Uncertain significance (Feb 06, 2023)
12-50396337-T-C		not specified	Likely benign (Jun 21, 2023)
12-50396345-A-G		not specified	Uncertain significance (Sep 29, 2022)
12-50396384-C-T		not specified	Uncertain significance (Aug 17, 2021)
12-50396397-G-C		not specified	Uncertain significance (Jul 25, 2023)
12-50396414-A-G		not specified	Uncertain significance (May 14, 2024)
12-50401021-T-A		not specified	Uncertain significance (Jan 11, 2023)
12-50401022-C-A		not specified	Uncertain significance (Feb 14, 2024)
12-50429010-A-G		not specified	Uncertain significance (Dec 22, 2023)
12-50429022-T-C		not specified	Uncertain significance (Aug 10, 2021)
12-50429085-T-G		not specified	Uncertain significance (Mar 07, 2024)
12-50430516-C-T		not specified	Uncertain significance (May 13, 2024)
12-50435497-G-C		not specified	Uncertain significance (Jun 17, 2024)
12-50437743-A-G		not specified	Uncertain significance (Jun 26, 2023)
12-50437743-A-T		not specified	Uncertain significance (Mar 01, 2023)
12-50437774-T-C		not specified	Uncertain significance (Apr 13, 2023)
12-50440495-T-G		not specified	Uncertain significance (Apr 12, 2022)
12-50453608-C-T		not specified	Uncertain significance (Aug 26, 2022)
12-50453614-A-G		not specified	Uncertain significance (Apr 23, 2024)
12-50453622-G-T		not specified	Uncertain significance (Oct 29, 2021)
12-50453649-A-G		not specified	Likely benign (Dec 27, 2023)
12-50453652-C-T		not specified	Uncertain significance (Nov 09, 2021)
12-50453665-C-T		not specified	Uncertain significance (Jan 30, 2024)
12-50453667-C-G		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LARP4	protein_coding	protein_coding	ENST00000398473	16	87622

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.869	0.131	124769	0	24	124793	0.0000962

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.988	327	381	0.858	0.0000185	4724
Missense in Polyphen		57	89.528	0.63667		1207
Synonymous	0.146	125	127	0.984	0.00000589	1382
Loss of Function	4.85	8	41.9	0.191	0.00000234	486

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000949	0.0000928
European (Non-Finnish)	0.000154	0.000150
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA binding protein that binds to the poly-A tract of mRNA molecules (PubMed:21098120). Associates with the 40S ribosomal subunit and with polysomes (PubMed:21098120). Plays a role in the regulation of mRNA translation (PubMed:21098120). Plays a role in the regulation of cell morphology and cytoskeletal organization (PubMed:21834987, PubMed:27615744). {ECO:0000269|PubMed:21098120, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:27615744}.

Intolerance Scores

• loftool: 0.672
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.58

Haploinsufficiency Scores

• pHI: 0.316
• hipred: N
• hipred_score: 0.494
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.443

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Larp4

Gene ontology

• Biological process: translation;cytoskeleton organization;regulation of cell morphogenesis;positive regulation of translation
• Cellular component: cytosol;polysome;cytoplasmic stress granule;membrane;cytosolic small ribosomal subunit
• Molecular function: RNA binding;protein binding;poly(A) binding