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.

not_specified (72 variants)
not_provided (2 variants)

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. These statistics are base on transcript: NM_000018357.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	1 clinvar	3
missense			71 clinvar			71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	71	2	1

Loading clinvar variants...

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
Phenotype

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