LARP7

La ribonucleoprotein 7, transcriptional regulator, the group of RNA binding motif containing|7SK snRNP complex|La ribonucleoproteins

Basic information

Region (hg38): 4:112637077-112657696

Links

ENSG00000174720

∙ NCBI:51574 ∙ OMIM:612026 ∙ HGNC:24912 ∙ Uniprot:Q4G0J3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

microcephalic primordial dwarfism, Alazami type (Definitive), mode of inheritance: AR
microcephalic primordial dwarfism, Alazami type (Moderate), mode of inheritance: AR
microcephalic primordial dwarfism, Alazami type (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Alazami syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	22865833; 30006060

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LARP7 gene.

not_provided (223 variants)
Inborn_genetic_diseases (74 variants)
Microcephalic_primordial_dwarfism,_Alazami_type (52 variants)
LARP7-related_disorder (9 variants)
Intellectual_disability (5 variants)
not_specified (3 variants)
Alazami-Yuan_syndrome (1 variants)
Epileptic_encephalopathy (1 variants)
Abnormal_brain_morphology (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LARP7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016648.4. 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			1 clinvar	52 clinvar		53
missense	1 clinvar	2 clinvar	108 clinvar	8 clinvar	1 clinvar	120
nonsense	12 clinvar	2 clinvar				14
start loss						0
frameshift	43 clinvar	19 clinvar	2 clinvar			64
splice donor/acceptor (+/-2bp)	2 clinvar	7 clinvar				9
Total	58	30	111	60	1

Highest pathogenic variant AF is 0.0000563792

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LARP7	protein_coding	protein_coding	ENST00000509061	13	20629

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.34e-8	0.982	125628	0	120	125748	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.268	297	284	1.04	0.0000134	3890
Missense in Polyphen		74	97.722	0.75725		1392
Synonymous	-2.06	118	92.7	1.27	0.00000438	1025
Loss of Function	2.22	16	28.9	0.554	0.00000141	422

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000780	0.000752
Ashkenazi Jewish	0.000333	0.000298
East Asian	0.000575	0.000544
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.000625	0.000580
Middle Eastern	0.000575	0.000544
South Asian	0.000714	0.000653
Other	0.000734	0.000652

dbNSFP

Source: dbNSFP

Function: FUNCTION: Negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system. Within the 7SK RNP complex, the positive transcription elongation factor b (P-TEFb) is sequestered in an inactive form, preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation. {ECO:0000269|PubMed:18249148, ECO:0000269|PubMed:18483487}.;
Disease: DISEASE: Alazami syndrome (ALAZS) [MIM:615071]: A syndromic form of primordial dwarfism, a condition characterized by severe growth restriction that has its onset in utero, and results in short stature and undersize. ALAZS patients manifest severe intellectual disability and distinct facial features including malar hypoplasia, deep-set eyes, broad nose, short philtrum, and macrostomia. Some patients have non-specific and inconsistent skeletal findings, for example, scoliosis and mild epiphyseal changes in the proximal phalanges, but no frank dysplasia. {ECO:0000269|PubMed:21937992, ECO:0000269|PubMed:22865833}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.113

Intolerance Scores

loftool: 0.969
rvis_EVS: 0.24
rvis_percentile_EVS: 69.46

Haploinsufficiency Scores

pHI: 0.499
hipred: Y
hipred_score: 0.659
ghis: 0.563

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Larp7
Phenotype: growth/size/body region phenotype; cellular phenotype; embryo phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Zebrafish Information Network

Gene name: larp7
Affected structure: atrium
Phenotype tag: abnormal
Phenotype quality: dilated

Gene ontology

Biological process: RNA processing
Cellular component: nucleoplasm;cytosol;ribonucleoprotein complex
Molecular function: RNA binding;protein binding