LARP1

protein-coding

La ribonucleoprotein 1, translational regulator, the group of MicroRNA protein coding host genes|La ribonucleoproteins

Gene summary

Enables several functions, including RNA binding activity; eukaryotic initiation factor 4E binding activity; and ribosomal small subunit binding activity. Involved in several processes, including TORC1 signaling; cellular response to rapamycin; and post-transcriptional regulation of gene expression. Located in TORC1 complex; cytoplasmic stress granule; and cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_033551.3

Inheritance

ClinVar variants

U:115B:7

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr5:154,682,986-154,817,605

External References & Databases

Ensembl (ENSG00000155506)

Transcript & Mutation Effects

hg38 • Region Span ~134.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LARP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 109

not providedTotal: 4

LARP1-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033551.3. 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	1 clinvar	4
missense			107 clinvar	5 clinvar		112
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	115	6	1	122

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033551.3	RefSeq	NP_291029.2	19	MANE Select
ENST00000518297.6	Ensembl	ENSP00000428589.2	19	MANE Select
NM_001367713.1	RefSeq	NP_001354642.1	16	Standard
NM_001367714.1	RefSeq	NP_001354643.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

translational initiation
cell population proliferation
positive regulation of macroautophagy
negative regulation of translation
TOR signaling

Molecular Function

RNA cap binding
RNA binding
mRNA 3'-UTR binding
protein binding
eukaryotic initiation factor 4E binding

Cellular Component

cytoplasm
polysome
cytoplasmic stress granule
membrane
TORC1 complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000336314
Coding exons: 19
Length: 104706
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125748
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.07	406	621	0.654	0.0000385	6684
Missense (PolyPhen)		166	297.58	0.55783		2987
Synonymous	0.911	207	224	0.923	0.0000126	1996
Loss of Function	6.41	4	55.6	0.0720	0.00000327	595

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: RNA-binding protein that promotes translation of specific classes of mRNAs downstream of the mTORC1 complex (PubMed:24532714, PubMed:25940091). Associates with the mRNA 5'cap in an MTOR-dependent manner and associates with mRNAs containing a 5' terminal oligopyrimidine (5'TOP) motif, which is present in mRNAs encoding for ribosomal proteins and several components of the translation machinery (PubMed:24532714, PubMed:25940091, PubMed:26206669). Associates with actively translating ribosomes via interaction with PABPC1/PABP and stimulates translation of mRNAs containing a 5'TOP, thereby regulating cell growth and proliferation (PubMed:20430826, PubMed:25940091). Positively regulates the replication of dengue virus (DENV) (PubMed:26735137). {ECO:0000269|PubMed:20430826, ECO:0000269|PubMed:24532714, ECO:0000269|PubMed:26206669, ECO:0000269|PubMed:26735137}.;

Recessive Scores

pRec: 0.0905

Intolerance Scores

LoFtool: 0.573
RVIS EVS: -1.35
RVIS percentile EVS: 4.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.905

Gene Damage Prediction

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