LHFPL2
Basic information
Region (hg38): 5:78485215-78770021
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHFPL2 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 0 |
Variants in LHFPL2
This is a list of pathogenic ClinVar variants found in the LHFPL2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-78488996-G-C | not specified | Uncertain significance (Apr 10, 2023) | ||
| 5-78489015-C-A | not specified | Uncertain significance (Dec 19, 2022) | ||
| 5-78489098-C-A | not specified | Uncertain significance (May 01, 2023) | ||
| 5-78509948-A-G | not specified | Uncertain significance (Nov 17, 2022) | ||
| 5-78510009-G-A | not specified | Uncertain significance (Apr 04, 2023) | ||
| 5-78510039-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
| 5-78510057-A-C | not specified | Uncertain significance (Feb 28, 2024) | ||
| 5-78510093-G-A | not specified | Uncertain significance (Mar 24, 2023) | ||
| 5-78510108-C-G | not specified | Uncertain significance (Oct 10, 2023) | ||
| 5-78510120-C-G | not specified | Uncertain significance (Jul 14, 2023) | ||
| 5-78510141-G-A | not specified | Uncertain significance (Mar 15, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LHFPL2 | protein_coding | protein_coding | ENST00000380345 | 2 | 284807 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0562 | 0.873 | 125738 | 0 | 10 | 125748 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.05 | 104 | 139 | 0.749 | 0.00000770 | 1481 |
| Missense in Polyphen | 32 | 54.169 | 0.59074 | 646 | ||
| Synonymous | 0.184 | 56 | 57.8 | 0.969 | 0.00000373 | 462 |
| Loss of Function | 1.51 | 3 | 7.45 | 0.403 | 3.19e-7 | 78 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000123 | 0.000123 |
| Ashkenazi Jewish | 0.000205 | 0.000198 |
| East Asian | 0.0000556 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000356 | 0.0000352 |
| Middle Eastern | 0.0000556 | 0.0000544 |
| South Asian | 0.0000328 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in female and male fertility. Involved in distal reproductive tract development. {ECO:0000250|UniProtKB:Q8BGA2}.;
- Pathway
- TYROBP Causal Network;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.559
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.12
Haploinsufficiency Scores
- pHI
- 0.411
- hipred
- N
- hipred_score
- 0.459
- ghis
- 0.559
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.240
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lhfpl2
- Phenotype
- reproductive system phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); digestive/alimentary phenotype; hearing/vestibular/ear phenotype; vision/eye phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- platelet degranulation;single fertilization;biological_process;development of primary female sexual characteristics;development of primary male sexual characteristics;positive regulation of fertilization
- Cellular component
- cellular_component;plasma membrane;integral component of membrane;platelet alpha granule membrane
- Molecular function
- molecular_function