LIPH

lipase H, the group of Lipases

Basic information

Region (hg38): 3:185506262-185552588

Links

ENSG00000163898

∙ NCBI:200879 ∙ OMIM:607365 ∙ HGNC:18483 ∙ Uniprot:Q8WWY8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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: CGD

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 ClinVar and linked to the LIPH gene.

Woolly hair, autosomal recessive 2, with or without hypotrichosis (2 variants)
not provided (2 variants)
Hypotrichosis 7 (1 variants)
LIPH-related disorder (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 clinvar	4 clinvar	15
missense		2 clinvar	26 clinvar	1 clinvar	1 clinvar	30
nonsense		1 clinvar				1
start loss						0
frameshift	1 clinvar	1 clinvar				2
inframe indel	1 clinvar					1
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding				1 clinvar	19 clinvar	20
Total	2	4	26	13	24

Highest pathogenic variant AF is 0.0000525

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.

Position	Phenotype	Significance	ClinVar
3-185508608-A-G		Benign (Nov 12, 2018)	1179532
3-185508704-C-T		Benign (Jun 19, 2021)	1178899
3-185508849-G-A		Likely benign (May 04, 2022)	2170244
3-185509120-G-A		Benign (Nov 12, 2018)	1277965
3-185511264-A-G		Benign (Jun 19, 2021)	1288941
3-185511530-G-A	Inborn genetic diseases	Uncertain significance (May 09, 2023)	2510895
3-185511578-C-T		Uncertain significance (Apr 29, 2022)	2128415
3-185511592-A-G		Likely benign (Nov 27, 2023)	2189956
3-185511644-T-C	Inborn genetic diseases	Uncertain significance (Sep 17, 2021)	2403394
3-185511657-G-A	not specified	Likely benign (Apr 07, 2023)	288240
3-185511676-T-C		Benign (Jan 31, 2024)	1228610
3-185511704-G-A		Likely benign (Oct 13, 2023)	2960052
3-185511969-C-T		Benign (Nov 12, 2018)	1240580
3-185513447-GTGGAGAAACTGGATCCTGTATGCACCATCAGTGGGATTGGAAAATTGTGCAACCATTAAGGAAAACAGTATAGTGGTGTCTCAAAAAATTAAAAAGAGAACTACAATATGATCCAGAAACTCCACTTCTGGATACAAGTCCAAAAAAATTGAAAGCAGAGTCTCAGACATTTGCACACCCATGTTCATAGCAGCACTAGTCACAATAGCCAAGAGGAGGAGGCAACCCAAGTGTTCATTGATGGAAGAATAAACAAAATGTGGTATATGCATATAATCAAATATTACTCAGCCTTAAAAATGAAGGAAATCAGCCAGGCGCGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAAGCCGAGGCGGGCAGATCATGAAGTCAGGAGTTTGAGACCAGCCTGGCCAGCACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTATCTGGGCATGGTGGCATGTGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGAGGAGGTTGCAGTGAGCTGAGATGTTTTGATGTATGTATACAATGTGGGATAATTAAATCAGCATATTCATTTGTTGTTTAAATCCTTTATCGAAAACAAGGATAACTTTTGTATTACATGTTTAATCAAAGGAAGTAAGGAGGAGAGGAACAAAGGGAGAAAGAGAGGGAAAGAGGGAGGAAAGGAAGGAAAAAGGGAGGAAGCAAAGAAAGGAAGAAGAGAAGGAGGGAAGGAAAGAAAACCCTTGCACCAATCCCATTTGTAAAGACCCTGGGAGATCAAGAACCAGGGAAGCAACTAAGCAATAGTTCCCCTTATATCTTTTATAGAACAAGGAAAAGCATAGATCTATAAATAAGAAAGTAGGTGGATTTGTGATTTAATTTCTCTGAGCAAAAAGGGAAATAGCGCACTGCAAACAATTGTAACTCAACTTACTGATTGATTTTGGATTCTGTGGTGTTTCCAGCTTTGTCTCTCAATTTGATGGTAATGTCCCCTCTTCTTACATTCTTGTTCCATGTTATAATATCCACAAAGTAATGATACACTGCAAAACAGAGAGAGAACACGGTAAGAGAGAGATACTACCAACTGATCCCCTGAAGGGCTGGTTCCTAAAAACTGAACCTCCCTAATCACTGAGTCTCTTCTTCTCTTTCTCTCTGGTTTCTCTGCAAAGATCCAGGGCAGAAGTTTCTAATATTCCCTTCTCTTCTCTTTGGTAAAGATGGCATGAGTGATAGCAGAGTTCATTGGTTTCCAGTCACCATGGTCAGGCATCATCGTTGAACCAGTGTTTCCAGGTATTGTGAAGTCTTAGGGCTTATGGCTGAGTGTGGTTCACATCAATTCCTGCCCATTTTAGACTCAACCAACTAAGGGGCCATTCGGAGACCCTCCAGGGCTGAGACGGTTTTCCACAGTTTGGGCCAAGTCCACCAGCCTACTCAGCCTTCCTCATCCTTCTCCCAATCATGCTCCACCACCTGCACTCCCTGCACTGTGAAGGCTCCTGGGCCTTCACCCACCTGGGCACGCTTACTTTGCCAGCTCTGTGAATCCACCTTTTAGGTTTCAACTTAATGTCATTCCTCCAGAAGGCTTTTCCTGACCCCCAGACTAAGTCAGGTCTCCTTTCTTGAAGTTCCTGCCATACTCTGGACTCTCCCCATTATTATTCAGCACACTTTCCTGTATTTACAAAATGCAAGAAAGGGTGATAATAAAAATAAAGTGGCATTCCCTAACCAGCAGACTCAGAGAAAAAAAAAGTGGTGAATATGTGGGTACATCTATACAAATGTTACCTGAATAATGTCTTATGGGTTTTTTTAAAAAAAAAAAAGATAAAATTAAAACACGCTACAACAGGAACTAATCAGGGAGATGACAGTCCCACGAAGGAATAAGGTCAGTCCTGGATTTGCCATTTTATGGCCCAACTTGCTCAGGGGCTTGCCCCATACAGACCAGGTAGGTGCCAAATCCTGGGCTGCCACACATGGCTCCAAAGAAAGAGGGAAACCCAGTGATCTGCAGGCTTTTTTTTTTTTTAAAAGAATCTCTCTGTGTTGCCCAGGCTGGAGTGCAGTGGCGTAATCTCGGTTCACGGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCAGCCTCAGCCTTCTAGGTAGCTGGGATTACAGGCAAGCACCACCACGCCCAGCTAATTTTTATATTTTGTTTTTGGGGTTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGGCCTCAAGTGATCCGCCCGCCTTGGCCTCCCAAAATGCTGGGAATGCAGGCGTGAGCCACCATGCTTAGCCTCCAGGCTCTTTTAAAAGAGTTGCTCACACCTGGCATGGAAGTTCACACCTGTAATCCCAGCACTAAGGCAGGAGGATTGCTTGAGCCCAAGAGTTCAAGACCAGCCTATGCAACATAGTGAGATTCTGTCTCTAAAAGAAACAAAAAAAACAGTTAGCTGGGCATGGTGGCGCATGCCCGAAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGGATTGCTTGAGTCCAGGAGGTTGAGGCTGCAGTGCCCCATTATTGTGCCACTGCACTCCAGCCTGGGTGACAGAACAAGACCCTGTCTCAAAAAAAAATTAACATAGCCTGGGCATGGTGGCTGATGCCTGTAATCCCAGCGCTTTGAGAGGCCAAGGCAGGCAGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGCAAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGATGCACACCTGTAGTCTCAGGTACTCGGAATCCTGAGGCAGGAGGATCGCGTGAACCCAGGAGGCAGAGATTGCAGTGAGCTGAGATTGCGCCACTGAACTTCAACTTGGGTGACAGAGTGAGACCCTGTCTCAAAAAAAATAAATAAAATGAAATAAAATAGTTGTTCCCAAGGAAAGTGAAAATGGGTACAAGACTGTAGGAAAAACACATCTGCCCAAGGAAATTCTAGTTGCTTCCCAAGGCGTCTAATCATTGGCTGCCCCCTTTAATTCCCATCTGGAATACTCAACCTCTCGAGGCCTTTGGGTCATCATGTTTGCTTTAGAGCTGGAACTGACCTGTAGATATGGCTGACACCTGATTTTTCCTAGTCTTAATTTTATGTCTTTTGGGGAATCAAGCAATTTTCTGGAAGATCTTAGTGATTAGAATGGTCATCCAGTGAAACTAACAACTCTGATTTGTTGAGATTTTATTAAATTAATATTTTTAAATGGCATCAGATTAAACCTAATATCCCAGAATACAGGCATTATTACCCCCATTTGACCAGTCAGGACATTGAGACTCAGAGAAGTCAAATGACTTCACCAAGGTCCCACAGCTATTATGTGGTAGACTCAGGAGTCAACCGAGGCCCTTCCAGCTCCAAAGTTGATGCTTCATCATGGCTCTTATTTGCCAAGAAGTAGCCAGGAAGCTGAGACTCAGCCATCCCCAAAATGAGAGTTAGGCAAAAGCCAACAACCACATTCACCACTCACTGCAGAATGGGCTCTCCTCAGCTGTGTCAAAGAATGCCTTCGTCATTGGAGGATCTTTCCCCCTTAGATGGTCTTTCCAATTATCAGCATAATAGCCTATGAAACAAGTTTAAAAAATTGTAAGATTAATATGTATTATACAAACATAAAAGCAACTGAGGTAGCAAGAACATTGAGTTTGACTGTATCCACCACTTCTGAGAGAAACTCCATCCCACCTCCATCCCCCATGGTGAGGGCCTGCAGGGTGACCCATCTTGCTGGCCAACCCTGTCCCTAAGAGCTGAAGGGCAACAGGACCCTCCAGTTGTTTTCCCCCTTTACTGGTTCTCAGTAGCAGGGTGGAGAGGTGTGGGGTGTGGCACACACTGGTGTGGACTAAAAATAACACTGACATTTTTCAGTAATACATTCATTTTCTAGATTAAAACAGATTCAAGTTCATACCTAAAATAGCATCACTCTTGAAAACCAATATGCTTTCTTGAAGAACTACAATGGGGCCCCTAAATTGCATAGACCTGGGCTTGCCACATGACTGACTGTGTCACTAAGCAGGTGAGTGTCCTCCTTTGTTTTTGCTGTCCAGAGGGCCCTCTTTCTCTCCTCTGTCCCTAGCCCTAGAGAATGGCCTTCACATTCTGCCTTAATTGATCCAGGGTGGGACCCAGGCATCAGTATTGTGTTAAAACTCCTTAGGTGATTCTAAAGCACAATCAAGGTTGAGAACCCCTTGTCTATACCATGCCCTGTTGTTAACTTGGATTTTTCCTTTTGGAAAAAAAATAGAAAATCCTCATGACCATCCAGTTTCAAAGTCCTAACCACCTAGAATATCTGTACTAATCCCTAGCGAATATCCAAGCAGCCTCCACAATATCTATTACCTCACTCCACCTGCTGTACGTGCACACAAGAGCCAGAATGTGGAGTGAGGGCATTTACATAGACATGAGTCTGTGAAAAAGTTCACTTGTCAGGAGAGTCTCTGGGCTCATTGTGGACCCTCTCCCAGCAGAGAGGTTGTAAGCACAGAAAGGGTATTCCTGTCCCCACAGGAGCAGGCTACGTAGAGTGACTGTACCCTGGGTAAGCTTGGAAACTCTTCTGTAACCTTCTTTTCCATGCTAGAATAGAGGGTCCAGGGAGGCTGTACTGCCTTCTGGATGGAATACTCTACAGTTGCTTTTCTTTTCTTTTTTCTTTCTTTTGTTTGTTTGTTTGCTTTTTGAGACGGAGTTTCACTCTTGTTGCCCAGGCTGGAGTGCAATGGCGCGGTCTCAGCTCACTGTATCCTCCGTCTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTTCAGGCGCCCGCCACCATGCCCAGCTAATTTTTTTGTATTTTTAGTAGAGATGAGATATCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTTGTGATTCGCCCACCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCTACCATGCCCAGTCTACATTGCTTTCTAACACTGTTTATTAGTAGGAGACTAGAGTAGTTCAAAGAACAAATTGGCTAGAAAAAGCTGACTAGAAAAAAAAAGTCTATTTTTAAAATTTTTTTCTTTTTAAGAAATTTTTTTTTAAATTTTAACCTTTTATTTATTTATTTT-G	Woolly hair, autosomal recessive 2, with or without hypotrichosis • Hypotrichosis 7	Pathogenic (Mar 01, 2009)	3304
3-185514381-G-A		Benign (Nov 12, 2018)	1281519
3-185514451-C-T		Likely benign (Apr 25, 2022)	1958880
3-185514481-A-G		Likely benign (Jun 28, 2023)	2919509
3-185514496-T-C	Inborn genetic diseases	Uncertain significance (Feb 28, 2024)	2037509
3-185514507-C-T	Inborn genetic diseases	Uncertain significance (Jan 17, 2024)	3119079
3-185514509-A-G	Inborn genetic diseases	Uncertain significance (May 14, 2024)	3290820
3-185514861-T-C		Benign (Jun 19, 2021)	1251339
3-185517049-AC-A		Likely benign (Sep 05, 2023)	2756187
3-185517130-T-G		Likely benign (Oct 07, 2022)	2075731
3-185517132-A-G		Uncertain significance (Jun 09, 2023)	2712075
3-185517150-T-G	Hypotrichosis 7	Uncertain significance (Mar 25, 2024)	3064369

GnomAD

Source: gnomAD

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: dbNSFP

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