PSCA

prostate stem cell antigen, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 8:142670307-142682725

Links

ENSG00000167653 ∙ NCBI:8000 ∙ OMIM:602470 ∙ HGNC:9500 ∙ Uniprot:O43653 ∙ 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 PSCA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSCA 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						0
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	8	1	1

Variants in PSCA

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

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

Position	Type	Phenotype	Significance	ClinVar
8-142680513-C-T			Benign (Jul 02, 2018)
8-142680560-C-T		not specified	Uncertain significance (Dec 19, 2023)
8-142681327-G-A		not specified	Uncertain significance (Apr 24, 2024)
8-142681367-C-A		not specified	Uncertain significance (Jul 11, 2023)
8-142681405-T-G		not specified	Uncertain significance (Jan 29, 2024)
8-142681421-G-C		not specified	Uncertain significance (Jan 26, 2022)
8-142682029-A-C		not specified	Uncertain significance (Feb 22, 2023)
8-142682040-G-A		not specified	Uncertain significance (Apr 25, 2023)
8-142682062-A-T		not specified	Uncertain significance (Aug 30, 2021)
8-142682089-T-C		not specified	Uncertain significance (Nov 01, 2022)
8-142682121-G-A		not specified	Likely benign (Dec 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSCA	protein_coding	protein_coding	ENST00000301258	3	12417

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.169	0.654	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.152	71	67.5	1.05	0.00000427	708
Missense in Polyphen		24	21.078	1.1386		264
Synonymous	0.440	29	32.2	0.901	0.00000242	219
Loss of Function	0.809	1	2.33	0.429	9.85e-8	30

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the regulation of cell proliferation. Has a cell-proliferation inhibition activity in vitro. {ECO:0000269|PubMed:18488030}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.152

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.146
• ghis: 0.383

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.471

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psca
• Phenotype: neoplasm; hematopoietic system phenotype; normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: negative regulation of ERK1 and ERK2 cascade;regulation of neurotransmitter receptor activity
• Cellular component: extracellular region;plasma membrane;membrane;anchored component of membrane;extracellular exosome
• Molecular function: acetylcholine receptor binding