LPP

LIM domain containing preferred translocation partner in lipoma, the group of MicroRNA protein coding host genes|Zyxin family

Basic information

Region (hg38): 3:188153284-188890671

Links

ENSG00000145012 ∙ NCBI:4026 ∙ OMIM:600700 ∙ HGNC:6679 ∙ Uniprot:Q93052 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPP 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				3	6	9
missense			47	6	4	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					28	28
Total	0	0	47	9	38

Variants in LPP

This is a list of pathogenic ClinVar variants found in the LPP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-188405894-TTTC-T			Benign (Jun 19, 2021)
3-188405910-C-T			Benign (Jun 19, 2021)
3-188406031-T-G			Benign (Nov 12, 2018)
3-188406152-G-A		not specified	Uncertain significance (May 04, 2022)
3-188406179-C-G		not specified	Uncertain significance (Apr 17, 2024)
3-188406184-C-T		LPP-related disorder	Likely benign (Sep 26, 2023)
3-188406289-C-G		not specified	Uncertain significance (Mar 03, 2022)
3-188406308-G-T		not specified	Uncertain significance (Apr 26, 2023)
3-188406566-C-A			Benign (Jun 19, 2021)
3-188484697-A-C		not specified	Uncertain significance (Feb 15, 2023)
3-188484762-A-T			Benign (Nov 12, 2018)
3-188484794-G-T			Benign (Jun 19, 2021)
3-188524698-C-T		not specified	Uncertain significance (Dec 06, 2021)
3-188524776-C-T		not specified	Uncertain significance (Jan 04, 2022)
3-188524881-TTCCTTCCTTCCGTCCG-T			Benign (Jun 19, 2021)
3-188524885-TTCCTTCCGTCCG-T			Benign (Jun 19, 2021)
3-188524893-G-T			Benign (Jun 19, 2021)
3-188524905-T-G			Benign (Jun 20, 2021)
3-188524909-T-G			Benign (Jun 19, 2021)
3-188524913-T-G			Benign (Jun 19, 2021)
3-188524917-T-G			Benign (Jun 19, 2021)
3-188524971-C-CT			Benign (Jun 20, 2021)
3-188609166-C-T		LPP-related disorder	Likely benign (Aug 05, 2024)
3-188609167-A-G			Benign (Jun 09, 2021)
3-188609182-T-C		Acute myeloid leukemia • LPP-related disorder	Uncertain significance (Jan 13, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LPP	protein_coding	protein_coding	ENST00000312675	9	737389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00719	0.993	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.50	441	361	1.22	0.0000197	3923
Missense in Polyphen		165	167.66	0.98412		1777
Synonymous	-1.97	165	136	1.21	0.00000761	1277
Loss of Function	3.33	9	28.1	0.321	0.00000159	318

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000264	0.000264
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a structural role at sites of cell adhesion in maintaining cell shape and motility. In addition to these structural functions, it may also be implicated in signaling events and activation of gene transcription. May be involved in signal transduction from cell adhesion sites to the nucleus allowing successful integration of signals arising from soluble factors and cell-cell adhesion sites. Also suggested to serve as a scaffold protein upon which distinct protein complexes are assembled in the cytoplasm and in the nucleus. {ECO:0000269|PubMed:10637295, ECO:0000269|Ref.2}.
• Disease: DISEASE: Note=A chromosomal aberration involving LPP is associated with pulmonary chondroid hamartomas. Translocation t(3;12)(q27- q28;q14-q15) with HMGA2 is detected in pulmonary chondroid hamartomas.; DISEASE: Note=A chromosomal aberration involving LPP is associated with parosteal lipomas. Translocation t(3;12)(q28;q14) with HMGA2 is also shown in one parosteal lipoma.; DISEASE: Note=A chromosomal aberration involving LPP is associated with acute monoblastic leukemia. Translocation t(3;11)(q28;q23) with KMT2A/MLL1 is associated with acute monoblastic leukemia.
• Pathway: EGFR1;Stabilization and expansion of the E-cadherin adherens junction (Consensus)

Recessive Scores

• pRec: 0.159

Intolerance Scores

• loftool: 0.294
• rvis_EVS: 1.05
• rvis_percentile_EVS: 91.37

Haploinsufficiency Scores

• pHI: 0.245
• hipred: Y
• hipred_score: 0.543
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.848

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lpp
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

Zebrafish Information Network

• Gene name: lpp
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: cell adhesion;biological_process
• Cellular component: nucleus;cytosol;plasma membrane;focal adhesion
• Molecular function: protein binding;metal ion binding