PSAPL1

prosaposin like 1

Basic information

Region (hg38): 4:7430284-7434930

Links

ENSG00000178597 ∙ NCBI:768239 ∙ ∙ HGNC:33131 ∙ Uniprot:Q6NUJ1 ∙ 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 PSAPL1 gene.

• Inborn genetic diseases (41 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSAPL1 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				2		2
missense			38	3		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	5	0

Variants in PSAPL1

This is a list of pathogenic ClinVar variants found in the PSAPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-7433330-G-A		not specified	Uncertain significance (Oct 03, 2022)
4-7433352-A-T		not specified	Uncertain significance (Jun 28, 2022)
4-7433366-C-A		not specified	Uncertain significance (Nov 22, 2021)
4-7433379-C-T		not specified	Likely benign (Jan 06, 2023)
4-7433395-G-A			Likely benign (Feb 01, 2023)
4-7433405-C-A		not specified	Uncertain significance (Apr 10, 2023)
4-7433469-C-T		not specified	Uncertain significance (Aug 14, 2023)
4-7433477-G-T		not specified	Uncertain significance (Mar 01, 2023)
4-7433502-C-T		not specified	Uncertain significance (Feb 05, 2024)
4-7433531-A-G		not specified	Uncertain significance (Sep 01, 2021)
4-7433556-C-T		not specified	Uncertain significance (Jan 09, 2024)
4-7433606-C-T		not specified	Uncertain significance (Jul 25, 2023)
4-7433630-C-G		not specified	Uncertain significance (Oct 26, 2022)
4-7433700-T-C		not specified	Uncertain significance (Jun 09, 2022)
4-7433703-C-T		not specified	Uncertain significance (Oct 20, 2023)
4-7433724-C-G		not specified	Uncertain significance (May 17, 2023)
4-7433754-G-A		not specified	Uncertain significance (Nov 09, 2021)
4-7433763-G-A		not specified	Uncertain significance (Jun 23, 2021)
4-7433843-G-C		not specified	Uncertain significance (Jan 26, 2022)
4-7433864-A-G		not specified	Uncertain significance (Nov 01, 2022)
4-7433932-C-G		not specified	Uncertain significance (May 11, 2022)
4-7433970-G-C		not specified	Uncertain significance (Feb 07, 2023)
4-7433982-C-T		not specified	Uncertain significance (Jul 27, 2022)
4-7433983-G-A			Likely benign (Jul 01, 2022)
4-7434041-G-A		not specified	Uncertain significance (Nov 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSAPL1	protein_coding	protein_coding	ENST00000319098	1	4679

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.01	354	305	1.16	0.0000182	3348
Missense in Polyphen		76	68.407	1.111		819
Synonymous	-2.50	173	136	1.27	0.00000923	1047
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May activate the lysosomal degradation of sphingolipids. {ECO:0000250}.
• Pathway: Lysosome - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.491
• rvis_EVS: 0.92
• rvis_percentile_EVS: 89.57

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.146
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.209

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psapl1

Gene ontology

• Biological process: sphingolipid metabolic process;adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;regulation of lipid metabolic process;prostate gland growth;epithelial cell differentiation involved in prostate gland development
• Cellular component: extracellular space;lysosome;cytosol