DLGAP3

DLG associated protein 3

Basic information

Region (hg38): 1:34865436-34929650

Links

ENSG00000116544 ∙ NCBI:58512 ∙ OMIM:611413 ∙ HGNC:30368 ∙ Uniprot:O95886 ∙ 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 DLGAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DLGAP3 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	5	8
missense			1	2		3
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	6	5

Variants in DLGAP3

This is a list of pathogenic ClinVar variants found in the DLGAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-34867103-T-C			Uncertain significance (Mar 01, 2023)
1-34867111-C-T			Likely benign (Dec 18, 2018)
1-34868711-G-A			Benign (Jan 19, 2018)
1-34868798-G-A			Benign (Dec 31, 2019)
1-34885511-C-T			Benign (Apr 09, 2018)
1-34900163-G-A			Benign/Likely benign (Jan 01, 2024)
1-34904343-G-A			Likely benign (Jun 29, 2018)
1-34904382-G-A			Benign (Oct 10, 2018)
1-34904466-G-A			Benign (Dec 31, 2019)
1-34905129-A-AC			Likely benign (Jul 06, 2018)
1-34905250-G-T			Likely benign (Dec 17, 2018)
1-34905251-G-T			Likely benign (Dec 17, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DLGAP3	protein_coding	protein_coding	ENST00000373347	10	64150

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000194	125722	0	4	125726	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.63	415	595	0.697	0.0000379	6209
Missense in Polyphen		138	250.16	0.55164		2611
Synonymous	0.0292	256	257	0.998	0.0000165	2063
Loss of Function	5.32	1	35.0	0.0286	0.00000184	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000264
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: 0.112

Intolerance Scores

• loftool: 0.0590
• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.8

Haploinsufficiency Scores

• pHI: 0.342
• hipred: Y
• hipred_score: 0.825
• ghis: 0.657

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.558

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dlgap3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: signaling;modification of synaptic structure
• Cellular component: plasma membrane;postsynaptic density;cell junction;neuromuscular junction;postsynaptic membrane;glutamatergic synapse;cholinergic synapse
• Molecular function: amyloid-beta binding;protein binding