LRRC32
Basic information
Region (hg38): 11:76657524-76670747
Previous symbols: [ "D11S833E", "GARP" ]
Links
Phenotypes
GenCC
Source:
- cleft palate, proliferative retinopathy, and developmental delay (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Cleft palate, proliferative retinopathy, and developmental delay | 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 | Audiologic/Otolaryngologic; Craniofacial; Neurologic; Ophthalmologic | 30976112 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 10 | 11 | ||||
missense | 108 | 12 | 122 | |||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 2 | 108 | 22 | 2 |
Highest pathogenic variant AF is 0.00000136828
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
LRRC32 | protein_coding | protein_coding | ENST00000407242 | 2 | 13224 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00108 | 0.956 | 125732 | 0 | 16 | 125748 | 0.0000636 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.0889 | 393 | 398 | 0.987 | 0.0000256 | 4202 |
Missense in Polyphen | 68 | 91.561 | 0.74267 | 1261 | ||
Synonymous | -1.17 | 210 | 190 | 1.11 | 0.0000117 | 1526 |
Loss of Function | 1.78 | 7 | 14.3 | 0.491 | 7.74e-7 | 148 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000371 | 0.000369 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000557 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000644 | 0.0000615 |
Middle Eastern | 0.0000557 | 0.0000544 |
South Asian | 0.0000657 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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