DLGAP4
Basic information
Region (hg38): 20:36306336-36528637
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 7 | |||||
missense | 46 | 51 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 46 | 9 | 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) | ||
20-36431875-C-G | not specified | Uncertain significance (Aug 28, 2024) | ||
20-36431904-C-A | not specified | Uncertain significance (Jun 30, 2024) | ||
20-36432009-A-G | not specified | Uncertain significance (Nov 11, 2024) | ||
20-36432063-C-T | not specified | Uncertain significance (Jul 13, 2021) | ||
20-36432094-G-A | not specified | Uncertain significance (Mar 29, 2022) | ||
20-36432099-G-A | not specified | Uncertain significance (Jun 17, 2024) | ||
20-36432108-G-A | not specified | Uncertain significance (May 12, 2024) | ||
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 (Aug 12, 2024) | ||
20-36432355-G-A | not specified | Uncertain significance (Jan 04, 2022) | ||
20-36432372-C-G | not specified | Uncertain significance (Oct 08, 2024) | ||
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) | ||
20-36432522-C-T | not specified | Uncertain significance (Jun 25, 2024) | ||
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) |
GnomAD
Source:
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:
- 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
- Phenotype
Gene ontology
- Biological process
- signaling
- Cellular component
- plasma membrane;neuromuscular junction;glutamatergic synapse;cholinergic synapse;postsynaptic specialization
- Molecular function
- protein binding