DLGAP1

DLG associated protein 1

Basic information

Region (hg38): 18:3496032-4455307

Links

ENSG00000170579 ∙ NCBI:9229 ∙ OMIM:605445 ∙ HGNC:2905 ∙ Uniprot:O14490 ∙ 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 DLGAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DLGAP1 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			53			53
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	3	5

Variants in DLGAP1

This is a list of pathogenic ClinVar variants found in the DLGAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-3499189-AGCCGG-A		Inborn genetic diseases	Uncertain significance (Jun 12, 2019)
18-3499198-T-C		not specified	Uncertain significance (Oct 05, 2023)
18-3499206-G-A			Likely benign (Sep 01, 2022)
18-3499301-C-T		not specified	Uncertain significance (Sep 02, 2024)
18-3499352-C-T		not specified	Uncertain significance (May 10, 2024)
18-3502503-A-T		not specified	Uncertain significance (Mar 30, 2024)
18-3502560-A-G		not specified	Uncertain significance (Mar 17, 2023)
18-3502604-C-T		DLGAP1-related disorder	Likely benign (May 31, 2019)
18-3502620-G-T		not specified	Uncertain significance (Dec 21, 2023)
18-3534200-C-T		not specified	Uncertain significance (Jun 30, 2022)
18-3534201-G-A		DLGAP1-related disorder	Benign (Jun 21, 2018)
18-3534226-C-T		DLGAP1-related disorder	Benign (Mar 08, 2019)
18-3534227-G-A		not specified	Uncertain significance (May 27, 2022)
18-3534284-G-A		DLGAP1-related disorder	Benign (Feb 20, 2019)
18-3534303-G-C		not specified	Uncertain significance (Feb 16, 2023)
18-3534324-G-A		DLGAP1-related disorder	Benign (Feb 20, 2019)
18-3534397-G-A		not specified	Uncertain significance (Feb 28, 2024)
18-3534421-C-A		not specified	Uncertain significance (Nov 14, 2023)
18-3534426-A-G		DLGAP1-related disorder	Likely benign (Jun 20, 2018)
18-3534472-G-A		not specified	Uncertain significance (Jun 27, 2023)
18-3534478-C-T		not specified	Uncertain significance (Mar 27, 2023)
18-3534497-T-A		not specified	Uncertain significance (Dec 15, 2023)
18-3534521-C-G		not specified	Uncertain significance (Aug 23, 2021)
18-3534526-G-A		not specified	Uncertain significance (Nov 17, 2022)
18-3567570-A-G		DLGAP1-related disorder	Benign (Jun 21, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DLGAP1	protein_coding	protein_coding	ENST00000315677	10	959306

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00125	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.20	403	629	0.641	0.0000409	6388
Missense in Polyphen		102	241.06	0.42314		2551
Synonymous	0.943	252	272	0.927	0.0000194	1934
Loss of Function	5.25	5	41.5	0.121	0.00000243	413

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000603	0.0000462
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of the postsynaptic scaffold in neuronal cells.
• Pathway: Glutamatergic synapse - Homo sapiens (human);Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.0679
• rvis_EVS: -1.59
• rvis_percentile_EVS: 3.05

Haploinsufficiency Scores

• pHI: 0.792
• hipred: Y
• hipred_score: 0.749
• ghis: 0.641

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.790

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dlgap1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: chemical synaptic transmission
• Cellular component: cellular_component;plasma membrane;postsynaptic density;cell junction;postsynaptic membrane
• Molecular function: protein binding;protein-containing complex binding