DLGAP4

DLG associated protein 4

Basic information

Region (hg38): 20:36306335-36528637

Links

ENSG00000080845 ∙ NCBI:22839 ∙ OMIM:616191 ∙ HGNC:24476 ∙ Uniprot:Q9Y2H0 ∙ 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 DLGAP4 gene.

• Inborn genetic diseases (33 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DLGAP4 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				6	1	7
missense			33	1	2	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	7	3

Variants in DLGAP4

This is a list of pathogenic ClinVar variants found in the DLGAP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-36431803-G-A		not specified	Uncertain significance (Sep 21, 2023)
20-36431833-C-T		not specified	Uncertain significance (Jul 13, 2021)
20-36431844-G-A		not specified	Uncertain significance (Mar 07, 2024)
20-36431850-C-T		not specified	Uncertain significance (Jul 14, 2021)
20-36432063-C-T		not specified	Uncertain significance (Jul 13, 2021)
20-36432094-G-A		not specified	Uncertain significance (Mar 29, 2022)
20-36432199-C-T		not specified	Uncertain significance (Feb 27, 2024)
20-36432210-G-A			Benign (Dec 31, 2019)
20-36432282-A-G		not specified	Uncertain significance (May 13, 2022)
20-36432355-G-A		not specified	Uncertain significance (Jan 04, 2022)
20-36432411-C-T		not specified	Uncertain significance (Jan 16, 2024)
20-36432412-G-A		not specified	Uncertain significance (Aug 21, 2023)
20-36432450-G-A			Benign (Dec 29, 2017)
20-36432513-G-A		not specified	Uncertain significance (Apr 07, 2022)
20-36432526-C-T		not specified	Uncertain significance (May 18, 2022)
20-36432527-G-A			Likely benign (May 07, 2018)
20-36432527-G-C			Likely benign (Dec 31, 2019)
20-36432561-G-A		not specified	Uncertain significance (Sep 01, 2021)
20-36432626-C-A		not specified	Uncertain significance (Dec 28, 2022)
20-36436110-T-C		not specified	Uncertain significance (Dec 17, 2021)
20-36436134-G-A		not specified	Uncertain significance (Jul 14, 2021)
20-36436157-G-C		not specified	Uncertain significance (Apr 08, 2022)
20-36436163-G-A		not specified	Uncertain significance (May 26, 2022)
20-36436209-G-T		not specified	Uncertain significance (Jan 04, 2024)
20-36439758-C-A		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DLGAP4	protein_coding	protein_coding	ENST00000373913	11	262783

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00752	125737	0	8	125745	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.76	443	639	0.693	0.0000422	6413
Missense in Polyphen		144	246.72	0.58365		2520
Synonymous	0.0451	285	286	0.997	0.0000202	2045
Loss of Function	4.84	5	36.7	0.136	0.00000180	418

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000631	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the molecular organization of synapses and neuronal cell signaling. Could be an adapter protein linking ion channel to the subsynaptic cytoskeleton. May induce enrichment of PSD-95/SAP90 at the plasma membrane.
• Pathway: Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.117
• rvis_EVS: -0.72
• rvis_percentile_EVS: 14.26

Haploinsufficiency Scores

• pHI: 0.163
• hipred: Y
• hipred_score: 0.825
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.884

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dlgap4

Gene ontology

• Biological process: signaling
• Cellular component: plasma membrane;neuromuscular junction;glutamatergic synapse;cholinergic synapse;postsynaptic specialization
• Molecular function: protein binding