PSD

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

Basic information

Region (hg38): 10:102402617-102421539

Links

ENSG00000059915 ∙ NCBI:5662 ∙ OMIM:602327 ∙ HGNC:9507 ∙ Uniprot:A5PKW4 ∙ 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 PSD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSD 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				7	1	8
missense			45	2	2	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				1	1	2
Total	0	0	45	10	4

Variants in PSD

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

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

Position	Type	Phenotype	Significance	ClinVar
10-102403210-C-T		not specified	Uncertain significance (Mar 25, 2024)
10-102403214-G-A		not specified	Uncertain significance (Sep 01, 2021)
10-102403216-C-T		not specified	Uncertain significance (Mar 29, 2024)
10-102403234-C-T			Benign (May 15, 2018)
10-102403252-C-G		not specified	Uncertain significance (Jan 17, 2024)
10-102403261-C-T		not specified	Uncertain significance (May 23, 2023)
10-102403262-G-A		not specified	Uncertain significance (Jul 12, 2022)
10-102403262-G-C		not specified	Uncertain significance (Dec 21, 2022)
10-102403313-G-A		not specified	Uncertain significance (Feb 02, 2024)
10-102403325-C-T		not specified	Uncertain significance (Jul 27, 2021)
10-102403334-C-T		not specified	Uncertain significance (Jun 29, 2023)
10-102403360-G-A		not specified	Uncertain significance (Sep 24, 2024)
10-102403403-G-C		not specified	Uncertain significance (Dec 15, 2023)
10-102403861-T-C		not specified	Uncertain significance (Nov 10, 2024)
10-102403897-C-T		not specified	Uncertain significance (Sep 19, 2022)
10-102403916-C-T		not specified	Uncertain significance (Dec 06, 2021)
10-102403930-C-T		not specified	Uncertain significance (Sep 03, 2024)
10-102403972-C-T			Likely benign (Aug 09, 2018)
10-102403973-G-A		not specified	Uncertain significance (Sep 16, 2021)
10-102403973-G-C		not specified	Uncertain significance (Sep 01, 2021)
10-102403990-C-T			Likely benign (Mar 29, 2018)
10-102404603-C-A		not specified	Uncertain significance (Dec 21, 2023)
10-102404618-G-A		not specified	Uncertain significance (Sep 17, 2021)
10-102404919-C-T		not specified	Uncertain significance (Dec 06, 2024)
10-102405064-G-A			Likely benign (Apr 16, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSD	protein_coding	protein_coding	ENST00000020673	16	18921

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.904	0.0964	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	504	631	0.799	0.0000389	6501
Missense in Polyphen		170	271.95	0.62512		2786
Synonymous	0.140	260	263	0.989	0.0000158	2256
Loss of Function	4.93	8	42.8	0.187	0.00000252	462

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000492	0.0000462
European (Non-Finnish)	0.0000718	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000662	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor for ARF6 (PubMed:23603394). Induces cytoskeletal remodeling (By similarity). {ECO:0000250|UniProtKB:Q5DTT2, ECO:0000269|PubMed:23603394}.
• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.394
• rvis_EVS: -1.32
• rvis_percentile_EVS: 4.76

Haploinsufficiency Scores

• pHI: 0.115
• hipred: Y
• hipred_score: 0.671
• ghis: 0.621

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.849

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psd

Gene ontology

• Biological process: signal transduction;neuron projection development;regulation of ARF protein signal transduction
• Cellular component: cleavage furrow;ruffle membrane;dendritic spine;extrinsic component of postsynaptic endosome membrane;postsynaptic density, intracellular component
• Molecular function: ARF guanyl-nucleotide exchange factor activity;protein binding;phospholipid binding