LYPLAL1

lysophospholipase like 1

Basic information

Region (hg38): 1:219173868-219212865

Links

ENSG00000143353 ∙ NCBI:127018 ∙ OMIM:616548 ∙ HGNC:20440 ∙ Uniprot:Q5VWZ2 ∙ 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 LYPLAL1 gene.

• Inborn genetic diseases (12 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYPLAL1 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				1		1
missense			11	1	1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	1

Variants in LYPLAL1

This is a list of pathogenic ClinVar variants found in the LYPLAL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-219173919-A-C		not specified	Uncertain significance (Apr 28, 2022)
1-219173929-C-G		not specified	Uncertain significance (Apr 27, 2022)
1-219173954-G-A		not specified	Uncertain significance (Jan 31, 2022)
1-219173960-C-T			Likely benign (Jul 25, 2018)
1-219173961-T-C		not specified	Uncertain significance (Feb 23, 2023)
1-219179204-C-T		not specified	Uncertain significance (Apr 05, 2023)
1-219179217-A-G		not specified	Uncertain significance (Nov 09, 2021)
1-219193114-A-G		not specified	Uncertain significance (Jun 02, 2023)
1-219193144-A-G		not specified	Uncertain significance (Jan 10, 2022)
1-219210603-T-G		not specified	Uncertain significance (Nov 17, 2023)
1-219211495-C-T		not specified	Uncertain significance (Jul 22, 2022)
1-219211500-G-T		not specified	Uncertain significance (Dec 11, 2023)
1-219211505-G-A		not specified	Likely benign (Sep 07, 2022)
1-219211559-T-C		not specified	Uncertain significance (Dec 20, 2021)
1-219211603-C-G			Benign (Jul 23, 2018)
1-219211672-A-G		not specified	Uncertain significance (Mar 01, 2023)
1-219211687-A-G		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYPLAL1	protein_coding	protein_coding	ENST00000366928	5	39022

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000264	0.544	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.23	159	121	1.31	0.00000526	1537
Missense in Polyphen		48	40.606	1.1821		509
Synonymous	-0.483	48	43.9	1.09	0.00000198	439
Loss of Function	0.656	8	10.3	0.779	4.32e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.000155
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000280	0.000277
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.00105	0.00105
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has depalmitoylating activity toward KCNMA1. Does not exhibit phospholipase nor triacylglycerol lipase activity, able to hydrolyze only short chain substrates due to its shallow active site. {ECO:0000269|PubMed:22052940, ECO:0000269|PubMed:22399288}.

Recessive Scores

• pRec: 0.0773

Intolerance Scores

• loftool: 0.842
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• pHI: 0.0983
• hipred: N
• hipred_score: 0.159
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lyplal1
• Phenotype: skeleton phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: protein depalmitoylation;biological_process
• Cellular component: cytoplasm;cytosol
• Molecular function: lysophospholipase activity;palmitoyl-(protein) hydrolase activity;carboxylic ester hydrolase activity