PSD4

pleckstrin and Sec7 domain containing 4, the group of Pleckstrin homology domain containing|Pleckstrin and Sec7 domain containing

Basic information

Region (hg38): 2:113157324-113209396

Links

ENSG00000125637 ∙ NCBI:23550 ∙ OMIM:614442 ∙ HGNC:19096 ∙ Uniprot:Q8NDX1 ∙ 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 PSD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSD4 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			53	3		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	3	0

Variants in PSD4

This is a list of pathogenic ClinVar variants found in the PSD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-113182485-A-G		not specified	Uncertain significance (Jul 09, 2021)
2-113182488-C-A		not specified	Uncertain significance (Dec 30, 2023)
2-113182526-A-G		not specified	Uncertain significance (Oct 04, 2022)
2-113182638-A-T		not specified	Uncertain significance (Sep 08, 2023)
2-113182659-C-A		not specified	Uncertain significance (Jan 02, 2024)
2-113182676-C-T		not specified	Uncertain significance (Dec 14, 2021)
2-113182844-G-A		not specified	Uncertain significance (Jun 17, 2024)
2-113182871-C-T		not specified	Uncertain significance (Oct 12, 2021)
2-113182898-C-T		not specified	Uncertain significance (Apr 12, 2023)
2-113182899-G-A		not specified	Likely benign (Oct 06, 2022)
2-113182970-G-A		not specified	Uncertain significance (Jul 05, 2023)
2-113182982-A-G		not specified	Uncertain significance (Aug 17, 2021)
2-113182986-C-T		not specified	Uncertain significance (Dec 18, 2023)
2-113182991-G-A		not specified	Uncertain significance (Dec 12, 2023)
2-113183025-C-T		not specified	Uncertain significance (Jul 12, 2023)
2-113183064-C-A		not specified	Uncertain significance (Dec 12, 2023)
2-113183070-C-T		not specified	Uncertain significance (Aug 17, 2022)
2-113183111-G-C		not specified	Uncertain significance (Feb 02, 2022)
2-113183159-C-T		not specified	Uncertain significance (Nov 21, 2023)
2-113183213-G-A		not specified	Uncertain significance (Oct 13, 2023)
2-113183264-G-A		not specified	Uncertain significance (Dec 15, 2023)
2-113183310-C-T		not specified	Uncertain significance (May 18, 2023)
2-113183316-T-C		not specified	Uncertain significance (Jan 30, 2024)
2-113183330-C-T		not specified	Uncertain significance (May 03, 2023)
2-113185383-G-A		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSD4	protein_coding	protein_coding	ENST00000245796	16	52072

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.423	0.577	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.965	539	606	0.890	0.0000338	6824
Missense in Polyphen		160	222.98	0.71754		2501
Synonymous	0.0593	251	252	0.995	0.0000151	2148
Loss of Function	5.05	11	49.2	0.223	0.00000236	546

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000365	0.000364
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000802	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor for ARF6 and ARL14/ARF7. Through ARL14 activation, controls the movement of MHC class II-containing vesicles along the actin cytoskeleton in dendritic cells. Involved in membrane recycling. Interacts with several phosphatidylinositol phosphate species, including phosphatidylinositol 3,4-bisphosphate, phosphatidylinositol 3,5- bisphosphate and phosphatidylinositol 4,5-bisphosphate. {ECO:0000269|PubMed:12082148, ECO:0000269|PubMed:21458045}.
• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0778

Intolerance Scores

• loftool: 0.553
• rvis_EVS: 1.41
• rvis_percentile_EVS: 94.79

Haploinsufficiency Scores

• pHI: 0.0741
• hipred: N
• hipred_score: 0.270
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.656

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psd4

Gene ontology

• Biological process: regulation of ARF protein signal transduction
• Cellular component: membrane;cleavage furrow;ruffle membrane
• Molecular function: ARF guanyl-nucleotide exchange factor activity;phospholipid binding