LYPLAL1

lysophospholipase like 1

Basic information

Region (hg38): 1:219173869-219212865

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.

• not_specified (36 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. These statistics are base on transcript: NM_000138794.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			34	2	1	37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	3	1

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