LARP4

protein-coding

La ribonucleoprotein 4, the group of La ribonucleoproteins

Gene summary

Enables mRNA 3'-UTR binding activity and poly(A) binding activity. Involved in positive regulation of translation. Located in cytoplasmic stress granule and cytosolic small ribosomal subunit. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_052879.5

Inheritance

—

ClinVar variants

U:91B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr12:50,392,383-50,480,004

External References & Databases

Ensembl (ENSG00000161813)

Transcript & Mutation Effects

hg38 • Region Span ~87.6 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 LARP4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 85

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052879.5. 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						0
missense			84 clinvar	3 clinvar		87
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	91	3	0	94

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 141 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052879.5	RefSeq	NP_443111.4	16	MANE Select
ENST00000398473.7	Ensembl	ENSP00000381490.2	16	MANE Select
NM_001170803.2	RefSeq	NP_001164274.1	14	Standard
NM_001170804.2	RefSeq	NP_001164275.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

translation
cytoskeleton organization
regulation of cell morphogenesis
positive regulation of translation

Molecular Function

RNA binding
protein binding
poly(A) binding

Cellular Component

cytosol
polysome
cytoplasmic stress granule
membrane
cytosolic small ribosomal subunit

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398473
Coding exons: 16
Length: 87622
Individuals with no LoFs: 124769
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 124793
p: 0.0000962

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.988	327	381	0.858	0.0000185	4724
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000095	0.000093	rare
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: N
Indispensability score: 0.443

Gene Damage Prediction

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