PSD3

pleckstrin and Sec7 domain containing 3, the group of Pleckstrin and Sec7 domain containing|Pleckstrin homology domain containing

Basic information

Region (hg38): 8:18527302-19084730

Links

ENSG00000156011 ∙ NCBI:23362 ∙ OMIM:614440 ∙ HGNC:19093 ∙ Uniprot:Q9NYI0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• antecubital pterygium syndrome (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PSD3 gene.

• Inborn genetic diseases (34 variants)
• not provided (15 variants)
• PSD3-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSD3 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				3	3	6
missense			36	2	7	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	5	10

Variants in PSD3

This is a list of pathogenic ClinVar variants found in the PSD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-18535780-C-T		not specified	Uncertain significance (Aug 02, 2021)
8-18535807-C-T		not specified	Uncertain significance (May 24, 2023)
8-18535837-T-G		not specified	Uncertain significance (Aug 13, 2021)
8-18535840-G-A		not specified	Uncertain significance (Feb 10, 2022)
8-18535861-T-G		not specified	Uncertain significance (Jan 03, 2022)
8-18535864-G-A		not specified	Uncertain significance (Apr 07, 2022)
8-18535886-C-T		not specified	Uncertain significance (Oct 13, 2023)
8-18556275-G-A			Benign (Jul 31, 2018)
8-18556304-C-T		not specified	Uncertain significance (Aug 30, 2022)
8-18556314-C-A		not specified	Uncertain significance (Oct 16, 2023)
8-18556343-G-T		not specified	Uncertain significance (Dec 16, 2022)
8-18572557-G-C		not specified	Uncertain significance (Aug 08, 2022)
8-18572566-G-A		not specified	Uncertain significance (Mar 29, 2023)
8-18572584-A-C		not specified	Uncertain significance (Dec 15, 2022)
8-18572586-C-T		not specified	Uncertain significance (Oct 05, 2022)
8-18572665-C-T		not specified	Uncertain significance (Jan 30, 2024)
8-18575161-G-C		not specified	Uncertain significance (Nov 27, 2023)
8-18575177-C-T		not specified	Uncertain significance (Jan 26, 2022)
8-18575209-G-C		not specified	Uncertain significance (Apr 07, 2022)
8-18575278-T-G		not specified	Uncertain significance (Dec 20, 2023)
8-18632636-T-C		PSD3-related disorder	Uncertain significance (Jan 13, 2023)
8-18632675-G-C		not specified	Uncertain significance (Dec 19, 2022)
8-18632697-C-T		not specified	Uncertain significance (Feb 23, 2023)
8-18632726-C-T		not specified	Uncertain significance (Aug 23, 2021)
8-18632768-G-C		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSD3	protein_coding	protein_coding	ENST00000327040	16	557430

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00948	0.991	125729	0	16	125745	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.50	666	566	1.18	0.0000299	6859
Missense in Polyphen		196	216.67	0.90462		2601
Synonymous	-3.57	283	216	1.31	0.0000125	2004
Loss of Function	4.55	13	46.4	0.280	0.00000233	611

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.000140	0.000139
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.0000545	0.0000544
South Asian	0.000197	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor for ARF6. {ECO:0000250}.
• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.500
• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.97

Haploinsufficiency Scores

• pHI: 0.622
• hipred: N
• hipred_score: 0.270
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.787

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psd3

Gene ontology

• Biological process: regulation of ARF protein signal transduction
• Cellular component: postsynaptic density;cell junction;ruffle membrane;postsynaptic membrane
• Molecular function: ARF guanyl-nucleotide exchange factor activity