LRRC32

leucine rich repeat containing 32

Basic information

Region (hg38): 11:76657524-76670747

Previous symbols: [ "D11S833E", "GARP" ]

Links

ENSG00000137507NCBI:2615OMIM:137207HGNC:4161Uniprot:Q14392AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • cleft palate, proliferative retinopathy, and developmental delay (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Cleft palate, proliferative retinopathy, and developmental delayARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingAudiologic/Otolaryngologic; Craniofacial; Neurologic; Ophthalmologic30976112

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRRC32 gene.

  • not_specified (114 variants)
  • not_provided (15 variants)
  • LRRC32-related_disorder (4 variants)
  • Cleft_palate,_proliferative_retinopathy,_and_developmental_delay (3 variants)
  • Cleft_palate (1 variants)
  • Global_developmental_delay (1 variants)
  • Vitreoretinopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC32 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001128922.2. 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.

EffectPLPVUSLBBSum
synonymous
10
clinvar
1
clinvar
11
missense
1
clinvar
108
clinvar
12
clinvar
1
clinvar
122
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 2 108 22 2

Highest pathogenic variant AF is 0.00000136828

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LRRC32protein_codingprotein_codingENST00000407242 213224
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.001080.9561257320161257480.0000636
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.08893933980.9870.00002564202
Missense in Polyphen6891.5610.742671261
Synonymous-1.172101901.110.00001171526
Loss of Function1.78714.30.4917.74e-7148

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003710.000369
Ashkenazi Jewish0.000.00
East Asian0.00005570.0000544
Finnish0.000.00
European (Non-Finnish)0.00006440.0000615
Middle Eastern0.00005570.0000544
South Asian0.00006570.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Key regulator of transforming growth factor beta (TGFB1, TGFB2 and TGFB3) that controls TGF-beta activation by maintaining it in a latent state during storage in extracellular space (PubMed:19750484, PubMed:19651619, PubMed:22278742). Associates specifically via disulfide bonds with the Latency-associated peptide (LAP), which is the regulatory chain of TGF-beta, and regulates integrin-dependent activation of TGF-beta (PubMed:22278742). Able to outcompete LTBP1 for binding to LAP regulatory chain of TGF-beta (PubMed:22278742). Controls activation of TGF-beta-1 (TGFB1) on the surface of activated regulatory T-cells (Tregs) (PubMed:19750484, PubMed:19651619). Required for epithelial fusion during palate development by regulating activation of TGF-beta-3 (TGFB3) (By similarity). {ECO:0000250|UniProtKB:G3XA59, ECO:0000269|PubMed:19651619, ECO:0000269|PubMed:19750484, ECO:0000269|PubMed:22278742}.;

Recessive Scores

pRec
0.131

Intolerance Scores

loftool
0.414
rvis_EVS
-1.21
rvis_percentile_EVS
5.68

Haploinsufficiency Scores

pHI
0.210
hipred
N
hipred_score
0.234
ghis
0.594

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.412

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Lrrc32
Phenotype
hematopoietic system phenotype; immune system phenotype;

Zebrafish Information Network

Gene name
lrrc32
Affected structure
thrombocyte
Phenotype tag
abnormal
Phenotype quality
distributed

Gene ontology

Biological process
transforming growth factor beta receptor signaling pathway;positive regulation of gene expression;negative regulation of activated T cell proliferation;negative regulation of cytokine secretion;secondary palate development;regulation of transforming growth factor beta activation;regulation of transforming growth factor beta3 activation
Cellular component
extracellular space;nucleoplasm;integral component of plasma membrane;cell surface;extracellular matrix
Molecular function
protein binding;transforming growth factor beta binding