PSD2

pleckstrin and Sec7 domain containing 2, the group of Pleckstrin homology domain containing|Pleckstrin and Sec7 domain containing

Basic information

Region (hg38): 5:139795807-139844466

Links

ENSG00000146005 ∙ NCBI:84249 ∙ ∙ HGNC:19092 ∙ Uniprot:Q9BQI7 ∙ 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 PSD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSD2 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			50		2	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	0	3

Variants in PSD2

This is a list of pathogenic ClinVar variants found in the PSD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-139809492-C-T		not specified	Uncertain significance (Nov 08, 2022)
5-139809500-C-T			Benign (Feb 25, 2018)
5-139809526-G-A			Benign (Feb 25, 2018)
5-139809531-C-T		not specified	Uncertain significance (Apr 13, 2022)
5-139809532-G-A			Benign (Feb 25, 2018)
5-139809589-G-A		not specified	Uncertain significance (Oct 03, 2023)
5-139809696-G-A		not specified	Uncertain significance (Jan 27, 2022)
5-139809721-C-T		not specified	Uncertain significance (Aug 02, 2021)
5-139809768-G-T		not specified	Uncertain significance (Apr 09, 2024)
5-139809772-C-T		not specified	Uncertain significance (Mar 24, 2023)
5-139809801-C-G		not specified	Uncertain significance (Jun 22, 2024)
5-139813320-C-T		not specified	Uncertain significance (Jun 07, 2024)
5-139813322-G-A		not specified	Uncertain significance (Dec 15, 2023)
5-139813338-G-A		not specified	Uncertain significance (Apr 27, 2022)
5-139813388-C-T		not specified	Uncertain significance (Jun 17, 2024)
5-139813392-G-A		not specified	Uncertain significance (Jun 17, 2024)
5-139813437-C-T		not specified	Uncertain significance (Sep 19, 2022)
5-139813468-G-T		not specified	Uncertain significance (Aug 08, 2023)
5-139813496-C-T		not specified	Uncertain significance (Jun 10, 2024)
5-139813544-A-T		not specified	Uncertain significance (Dec 13, 2023)
5-139813587-A-G		not specified	Uncertain significance (Jun 18, 2021)
5-139813626-G-A		not specified	Uncertain significance (Sep 17, 2021)
5-139813658-A-G		not specified	Uncertain significance (Jul 12, 2022)
5-139813704-G-C		not specified	Uncertain significance (Oct 03, 2023)
5-139813730-G-A		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSD2	protein_coding	protein_coding	ENST00000274710	14	48646

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000221	1.00	125649	0	99	125748	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.430	456	483	0.945	0.0000301	5054
Missense in Polyphen		169	194.58	0.86853		2052
Synonymous	0.376	203	210	0.967	0.0000136	1583
Loss of Function	3.27	12	32.0	0.376	0.00000171	369

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000248	0.000241
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.000737	0.000693
European (Non-Finnish)	0.000646	0.000624
Middle Eastern	0.000164	0.000163
South Asian	0.0000342	0.0000327
Other	0.000511	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.490
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.12

Haploinsufficiency Scores

• pHI: 0.170
• hipred: Y
• hipred_score: 0.575
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.699

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psd2

Zebrafish Information Network

• Gene name: psd2
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: curved ventral

Gene ontology

• Biological process: regulation of ARF protein signal transduction
• Cellular component: integral component of membrane;dendrite;cleavage furrow;ruffle membrane;neuronal cell body;postsynapse;glutamatergic synapse
• Molecular function: ARF guanyl-nucleotide exchange factor activity;phospholipid binding