DLGAP2

DLG associated protein 2

Basic information

Region (hg38): 8:737627-1708476

Previous symbols: [ "ERICH1-AS1", "C8orf68" ]

Links

ENSG00000198010 ∙ NCBI:9228 ∙ OMIM:605438 ∙ HGNC:2906 ∙ Uniprot:Q9P1A6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DLGAP2 gene.

• Inborn genetic diseases (53 variants)
• not provided (11 variants)
• not specified (2 variants)
• DLGAP2-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DLGAP2 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	1	4
missense			53	1	3	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					2	2
Total	0	0	53	4	6

Variants in DLGAP2

This is a list of pathogenic ClinVar variants found in the DLGAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-737814-G-T		DLGAP2-related disorder	Benign (Sep 18, 2019)
8-907927-C-T		DLGAP2-related disorder	Likely benign (May 31, 2019)
8-1258864-G-A			Likely benign (Mar 01, 2023)
8-1501356-G-C		DLGAP2-related disorder	Likely benign (May 24, 2019)
8-1548627-C-T			Likely benign (Sep 01, 2022)
8-1548799-G-A		not specified	Uncertain significance (Dec 20, 2023)
8-1548860-C-T		not specified	Uncertain significance (Jul 14, 2021)
8-1548874-G-T		not specified	Uncertain significance (Apr 21, 2022)
8-1548885-G-T		DLGAP2-related disorder • not specified	Uncertain significance (Feb 08, 2024)
8-1548914-A-C		not specified	Uncertain significance (Jan 30, 2024)
8-1548962-A-G		not specified	Uncertain significance (Aug 08, 2022)
8-1548964-G-A		not specified	Benign (May 04, 2022)
8-1548973-G-A		not specified	Uncertain significance (Aug 23, 2021)
8-1548974-A-G		not specified	Uncertain significance (Sep 28, 2023)
8-1548979-T-C		not specified	Uncertain significance (May 09, 2023)
8-1548980-G-T		not specified	Uncertain significance (Apr 24, 2023)
8-1548992-A-C		not specified	Uncertain significance (Dec 28, 2022)
8-1549027-C-G		DLGAP2-related disorder	Uncertain significance (Dec 22, 2023)
8-1549094-G-A		DLGAP2-related disorder	Benign (Jul 10, 2019)
8-1549187-C-T		not specified	Uncertain significance (Aug 15, 2023)
8-1549189-C-G		not specified	Uncertain significance (Oct 03, 2022)
8-1549232-A-C		not specified	Uncertain significance (May 04, 2022)
8-1549258-G-A		not specified	Uncertain significance (Jun 11, 2021)
8-1549272-G-A		DLGAP2-related disorder	Likely benign (Aug 05, 2019)
8-1549375-A-C		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DLGAP2	protein_coding	protein_coding	ENST00000421627	11	207111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000114	124648	0	3	124651	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.996	711	640	1.11	0.0000442	6275
Missense in Polyphen		226	254.55	0.88786		2445
Synonymous	-5.48	422	301	1.40	0.0000253	1864
Loss of Function	5.35	3	39.1	0.0768	0.00000199	429

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000181	0.0000177
Middle Eastern	0.0000556	0.0000556
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: 0.110

Intolerance Scores

• loftool: 0.109
• rvis_EVS: -1.61
• rvis_percentile_EVS: 3

Haploinsufficiency Scores

• pHI: 0.183
• hipred: Y
• hipred_score: 0.695
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.712

Mouse Genome Informatics

• Gene name: Dlgap2
• 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)

Gene ontology

• Biological process: neuron-neuron synaptic transmission
• Cellular component: neurofilament;plasma membrane;postsynaptic density;cell junction;postsynaptic membrane
• Molecular function: protein binding