LIPH
Basic information
Region (hg38): 3:185506261-185552588
Links
Phenotypes
GenCC
Source:
- hypotrichosis 7 (Strong), mode of inheritance: AR
- isolated familial wooly hair disorder (Supportive), mode of inheritance: AD
- hypotrichosis simplex (Supportive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Hypotrichosis 7 | 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 | Dermatologic | 17095700; 17333281; 18445047; 19365138; 19892526; 21426374; 23590372 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (45 variants)
- Inborn genetic diseases (16 variants)
- Hypotrichosis 7 (4 variants)
- Woolly hair, autosomal recessive 2, with or without hypotrichosis (4 variants)
- not specified (1 variants)
- Hypotrichosis simplex (1 variants)
- LIPH-related condition (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIPH 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 | 11 | |||||
| missense | 20 | 24 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| inframe indel | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 1 | 1 | 2 | |||
| non coding ? | 19 | 20 | ||||
| Total | 2 | 4 | 20 | 9 | 24 |
Highest pathogenic variant AF is 0.0000854
Variants in LIPH
This is a list of pathogenic ClinVar variants found in the LIPH region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LIPH | protein_coding | protein_coding | ENST00000296252 | 10 | 46352 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 6.53e-11 | 0.235 | 125659 | 1 | 88 | 125748 | 0.000354 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.740 | 210 | 242 | 0.866 | 0.0000121 | 2973 |
| Missense in Polyphen | 79 | 86.105 | 0.91749 | 1057 | ||
| Synonymous | -0.0559 | 93 | 92.3 | 1.01 | 0.00000525 | 851 |
| Loss of Function | 0.805 | 18 | 22.1 | 0.815 | 0.00000109 | 277 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000612 | 0.000612 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000381 | 0.000326 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000352 | 0.000352 |
| Middle Eastern | 0.000381 | 0.000326 |
| South Asian | 0.00101 | 0.000980 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Hydrolyzes specifically phosphatidic acid (PA) to produce 2-acyl lysophosphatidic acid (LPA; a potent bioactive lipid mediator) and fatty acid. Does not hydrolyze other phospholipids, like phosphatidylserine (PS), phosphatidylcholine (PC) and phosphatidylethanolamine (PE) or triacylglycerol (TG). {ECO:0000269|PubMed:12063250, ECO:0000269|PubMed:12963729}.;
- Disease
- DISEASE: Woolly hair autosomal recessive 2 (ARWH2) [MIM:604379]: A hair shaft disorder characterized by fine and tightly curled hair. Compared to normal curly hair that is observed in some populations, woolly hair grows slowly and stops growing after a few inches. Under light microscopy, woolly hair shows some structural anomalies, including trichorrhexis nodosa and tapered ends. Some individuals may present with hypotrichosis. {ECO:0000269|PubMed:18830268}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA
(Consensus)
Intolerance Scores
- loftool
- 0.342
- rvis_EVS
- -0.31
- rvis_percentile_EVS
- 31.93
Haploinsufficiency Scores
- pHI
- 0.0701
- hipred
- N
- hipred_score
- 0.171
- ghis
- 0.499
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.208
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Liph
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); pigmentation phenotype;
Gene ontology
- Biological process
- phosphatidic acid biosynthetic process;lipid catabolic process
- Cellular component
- extracellular space;plasma membrane
- Molecular function
- phospholipase activity;heparin binding;carboxylic ester hydrolase activity