DLG2

discs large MAGUK scaffold protein 2, the group of Protein phosphatase 1 regulatory subunits|PDZ domain containing|Membrane associated guanylate kinases

Basic information

Region (hg38): 11:83455011-85628335

Links

ENSG00000150672 ∙ NCBI:1740 ∙ OMIM:603583 ∙ HGNC:2901 ∙ Uniprot:Q15700 ∙ 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 DLG2 gene.

• Inborn genetic diseases (17 variants)
• not provided (15 variants)
• DLG2-related condition (6 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DLG2 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				5	5	10
missense			22	2		24
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			2			2
splice region						0
non coding				1	1	2
Total	0	0	25	8	6

Variants in DLG2

This is a list of pathogenic ClinVar variants found in the DLG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-83459873-A-G		not specified	Uncertain significance (Jul 08, 2022)
11-83459894-A-G		not specified	Uncertain significance (Oct 13, 2023)
11-83459914-T-C			Benign (Jul 31, 2018)
11-83469202-C-T		not specified	Uncertain significance (Oct 17, 2023)
11-83471660-A-G			Benign/Likely benign (Jun 01, 2022)
11-83471683-G-C		not specified	Uncertain significance (May 08, 2023)
11-83471683-G-T			Benign (Jul 31, 2018)
11-83471718-G-A		not specified	Uncertain significance (Dec 06, 2021)
11-83484146-T-C		not specified	Uncertain significance (Aug 15, 2023)
11-83484229-CTG-C		DLG2-related disorder	Uncertain significance (Oct 27, 2022)
11-83541830-C-A		DLG2-related disorder	Uncertain significance (Jul 12, 2023)
11-83633227-G-A		not specified	Uncertain significance (Dec 13, 2022)
11-83786686-TGACC-T		DLG2-related disorder	Uncertain significance (Jun 07, 2023)
11-83786731-G-T		not specified	Uncertain significance (Jan 22, 2024)
11-83786734-C-G		not specified	Uncertain significance (May 24, 2023)
11-83786766-T-A			Benign (Jul 31, 2018)
11-83786767-G-A		not specified	Uncertain significance (Jan 08, 2024)
11-83833643-C-T		not specified	Uncertain significance (Feb 13, 2024)
11-83833699-C-T		not specified	Uncertain significance (Jun 03, 2022)
11-83874429-G-A		not specified	Uncertain significance (Sep 21, 2023)
11-83874439-G-A		not specified	Uncertain significance (Dec 28, 2023)
11-83874444-A-G		not specified	Likely benign (Sep 18, 2015)
11-83874451-T-C		not specified	Likely benign (May 17, 2023)
11-83874469-C-T		DLG2-related disorder	Likely benign (Dec 20, 2022)
11-83930380-C-G		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DLG2	protein_coding	protein_coding	ENST00000376104	26	2172912

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.708	0.292	125522	0	11	125533	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.08	400	535	0.747	0.0000287	6384
Missense in Polyphen		202	312.59	0.64622		3667
Synonymous	0.757	182	195	0.931	0.0000111	1814
Loss of Function	5.71	13	61.2	0.212	0.00000372	689

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000220	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.0000557	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for perception of chronic pain through NMDA receptor signaling. Regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord. Interacts with the cytoplasmic tail of NMDA receptor subunits as well as inward rectifying potassium channels. Involved in regulation of synaptic stability at cholinergic synapses. Part of the postsynaptic protein scaffold of excitatory synapses (By similarity). {ECO:0000250}.
• Pathway: Tight junction - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.145
• rvis_EVS: -1.6
• rvis_percentile_EVS: 3.04

Haploinsufficiency Scores

• pHI: 0.986
• hipred: Y
• hipred_score: 0.706
• ghis: 0.638

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.687

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dlg2
• 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: MAPK cascade;chemical synaptic transmission;negative regulation of phosphatase activity;sensory perception of pain;cellular response to potassium ion;receptor clustering;establishment or maintenance of epithelial cell apical/basal polarity;GMP metabolic process;GDP metabolic process;receptor localization to synapse;cell-cell adhesion;maintenance of postsynaptic density structure;anterograde axonal protein transport;retrograde axonal protein transport;neurotransmitter receptor localization to postsynaptic specialization membrane
• Cellular component: cytosol;plasma membrane;voltage-gated potassium channel complex;ionotropic glutamate receptor complex;postsynaptic density;membrane;basolateral plasma membrane;cell junction;neuromuscular junction;neuron projection;juxtaparanode region of axon;postsynaptic density membrane;glutamatergic synapse;axon cytoplasm
• Molecular function: guanylate kinase activity;Ras guanyl-nucleotide exchange factor activity;protein binding;kinase binding;ionotropic glutamate receptor binding;structural constituent of postsynaptic density