LARP6

La ribonucleoprotein 6, translational regulator, the group of La ribonucleoproteins

Basic information

Region (hg38): 15:70829130-70854157

Links

ENSG00000166173 ∙ NCBI:55323 ∙ OMIM:611300 ∙ HGNC:24012 ∙ Uniprot:Q9BRS8 ∙ 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 LARP6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LARP6 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
missense			38			38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	0	1

Variants in LARP6

This is a list of pathogenic ClinVar variants found in the LARP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-70832068-C-G		not specified	Uncertain significance (Dec 31, 2023)
15-70832078-G-C		not specified	Uncertain significance (Dec 31, 2023)
15-70832126-C-A		not specified	Uncertain significance (Sep 28, 2021)
15-70832150-T-C		not specified	Uncertain significance (Apr 20, 2024)
15-70832179-G-A		not specified	Uncertain significance (Dec 30, 2023)
15-70832221-C-T		not specified	Uncertain significance (Sep 22, 2023)
15-70832237-G-T		not specified	Uncertain significance (Jan 24, 2024)
15-70832281-C-T		not specified	Uncertain significance (Aug 16, 2021)
15-70832282-A-G		not specified	Uncertain significance (Jun 10, 2024)
15-70832288-G-A		not specified	Uncertain significance (Apr 29, 2024)
15-70832357-C-T		not specified	Uncertain significance (Jun 22, 2023)
15-70832363-G-T		not specified	Uncertain significance (Jul 09, 2021)
15-70832507-C-T		not specified	Uncertain significance (May 16, 2023)
15-70832606-C-T		not specified	Uncertain significance (May 10, 2022)
15-70832611-T-C		not specified	Uncertain significance (Jun 30, 2022)
15-70832671-A-G		not specified	Uncertain significance (Sep 29, 2023)
15-70832715-T-A		not specified	Uncertain significance (Jun 03, 2022)
15-70832771-C-G		not specified	Uncertain significance (Jun 14, 2024)
15-70832782-C-T		not specified	Uncertain significance (Nov 21, 2022)
15-70832827-T-C		not specified	Uncertain significance (Dec 21, 2023)
15-70832864-C-T		not specified	Uncertain significance (May 23, 2024)
15-70832870-G-T		not specified	Uncertain significance (Jul 26, 2022)
15-70832871-C-A		not specified	Uncertain significance (Sep 29, 2023)
15-70832927-C-T		not specified	Uncertain significance (Feb 13, 2024)
15-70832939-G-C		not specified	Uncertain significance (Oct 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LARP6	protein_coding	protein_coding	ENST00000299213	3	22636

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.669	0.330	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	197	266	0.740	0.0000159	3211
Missense in Polyphen		55	98.114	0.56057		1106
Synonymous	-0.300	115	111	1.04	0.00000700	983
Loss of Function	2.71	2	12.3	0.163	5.99e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000302	0.0000264
Middle Eastern	0.0000548	0.0000544
South Asian	0.00	0.00
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates the coordinated translation of type I collagen alpha-1 and alpha-2 mRNAs, CO1A1 and CO1A2. Stabilizes mRNAs through high-affinity binding of a stem-loop structure in their 5' UTR. This regulation requires VIM and MYH10 filaments, and the helicase DHX9. {ECO:0000269|PubMed:20603131, ECO:0000269|PubMed:21746880, ECO:0000269|PubMed:22190748}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.181
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.34

Haploinsufficiency Scores

• pHI: 0.172
• hipred: Y
• hipred_score: 0.768
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.728

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Larp6

Zebrafish Information Network

• Gene name: larp6a
• Affected structure: slow muscle cell
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: RNA processing;positive regulation of collagen biosynthetic process;positive regulation of translation;positive regulation of mRNA binding
• Cellular component: nucleus;cytoplasm;polysome;ribonucleoprotein complex
• Molecular function: protein binding;myosin binding;RNA stem-loop binding;mRNA 5'-UTR binding;sequence-specific mRNA binding