LARP4B

protein-coding

La ribonucleoprotein 4B, the group of La ribonucleoproteins

Gene summary

This gene encodes a member of an evolutionarily conserved protein family implicated in RNA metabolism and translation. Members of this family are characterized by the presence of an La motif, which is often located adjacent to one or more RNA recognition motifs (RRM). Together, the two motifs constitute the functional region of the protein and enable its interaction with the RNA substrate. This protein family is divided into five sub-families: the genuine La proteins and four La-related protein (LARP) sub-families. The protein encoded by this gene belongs to LARP sub-family 4. It is a cytoplasmic protein that may play a stimulatory role in translation. [provided by RefSeq, Oct 2012]

Previous symbols:

KIAA0217
LARP5

MANE transcript

NM_015155.3

Inheritance

—

ClinVar variants

P:1U:116B:13

Top phenotype

Myoepithelial tumor

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr10:806,933-931,821

External References & Databases

Ensembl (ENSG00000107929)

Transcript & Mutation Effects

hg38 • Region Span ~124.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LARP4B variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 109

not providedTotal: 9

Myoepithelial tumorTotal: 1

Autism spectrum disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015155.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar	2 clinvar	5
missense		1 clinvar	102 clinvar	10 clinvar		113
nonsense			2 clinvar			2
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	1	116	11	2	130

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 55 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015155.3	RefSeq	NP_055970.1	17	MANE Select
ENST00000316157.8	Ensembl	ENSP00000326128.3	17	MANE Select
NM_001351277.2	RefSeq	NP_001338206.1	17	Standard
ENST00000406525.6	Ensembl	ENSP00000385229.2	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of translation

Molecular Function

RNA binding
protein binding

Cellular Component

nucleolus
cytosol
cytoplasmic stress granule
membrane
polysomal ribosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000316157
Coding exons: 17
Length: 122081
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125745
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.94	326	441	0.740	0.0000265	4774
Missense (PolyPhen)		76	138.11	0.5503		1575
Synonymous	-0.0259	182	182	1.00	0.0000126	1482
Loss of Function	5.55	2	39.8	0.0503	0.00000206	457

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Stimulates mRNA translation. {ECO:0000269|PubMed:20573744}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.0360
RVIS EVS: -1.06
RVIS percentile EVS: 7.48

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.635

Gene Damage Prediction

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