PSPN

persephin, the group of GDNF family ligands

Basic information

Region (hg38): 19:6375148-6379058

Links

ENSG00000125650 ∙ NCBI:5623 ∙ OMIM:602921 ∙ HGNC:9579 ∙ Uniprot:O60542 ∙ 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 PSPN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSPN 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			24	2		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	0

Variants in PSPN

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

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

Position	Type	Phenotype	Significance	ClinVar
19-6375331-G-T		not specified	Uncertain significance (Nov 12, 2024)
19-6375337-C-T		not specified	Uncertain significance (Oct 19, 2024)
19-6375340-T-C		not specified	Uncertain significance (Aug 17, 2021)
19-6375346-C-T		not specified	Uncertain significance (Jan 17, 2025)
19-6375350-G-A		not specified	Uncertain significance (Mar 25, 2024)
19-6375353-G-A		not specified	Uncertain significance (Nov 15, 2024)
19-6375407-C-T		not specified	Uncertain significance (Nov 08, 2024)
19-6375427-T-C		not specified	Likely benign (Feb 16, 2023)
19-6375430-A-C		not specified	Uncertain significance (Dec 09, 2023)
19-6375433-C-T		not specified	Uncertain significance (May 01, 2024)
19-6375461-G-A		not specified	Uncertain significance (Jun 17, 2024)
19-6375469-C-G		not specified	Uncertain significance (May 14, 2024)
19-6375469-C-T		not specified	Uncertain significance (Aug 02, 2022)
19-6375481-C-T		not specified	Uncertain significance (Mar 31, 2024)
19-6375482-C-T		not specified	Uncertain significance (Jul 05, 2024)
19-6375485-C-T		not specified	Uncertain significance (Dec 21, 2023)
19-6375518-C-T		not specified	Likely benign (Mar 29, 2022)
19-6375589-C-T		not specified	Uncertain significance (Jan 10, 2023)
19-6375590-G-A		not specified	Uncertain significance (Nov 08, 2021)
19-6375595-C-T		not specified	Uncertain significance (Oct 27, 2023)
19-6375596-G-A		not specified	Uncertain significance (Jun 10, 2024)
19-6375607-C-T		not specified	Uncertain significance (Dec 06, 2022)
19-6375608-G-A		not specified	Uncertain significance (Dec 23, 2024)
19-6375753-C-G		not specified	Uncertain significance (Dec 13, 2023)
19-6375771-G-A		not specified	Uncertain significance (Mar 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSPN	protein_coding	protein_coding	ENST00000245810	2	3911

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000112	0.387	124543	0	4	124547	0.0000161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.252	80	86.6	0.924	0.00000618	922
Missense in Polyphen		24	31.448	0.76315		397
Synonymous	-0.757	46	39.9	1.15	0.00000269	361
Loss of Function	0.0797	6	6.21	0.965	4.08e-7	48

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000625	0.0000623
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000269	0.0000267
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits neurotrophic activity on mesencephalic dopaminergic and motor neurons.
• Pathway: Developmental Biology;Signal Transduction;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;NCAM signaling for neurite out-growth;NCAM1 interactions;RET signaling;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.148

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.146
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.407

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pspn
• Phenotype: homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: MAPK cascade;nervous system development;axon guidance;central nervous system development;regulation of signaling receptor activity
• Cellular component: extracellular region
• Molecular function: Ras guanyl-nucleotide exchange factor activity;signaling receptor binding;growth factor activity