DGCR2
Basic information
Region (hg38): 22:19036282-19122454
Links
Phenotypes
GenCC
Source:
- schizophrenia (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Schizophrenia | AD | General | Evidence or clinical applicability unclear | Neurologic | 21822266 |
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 DGCR2 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 | 6 | |||||
missense | 53 | 54 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 53 | 3 | 4 |
Variants in DGCR2
This is a list of pathogenic ClinVar variants found in the DGCR2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
22-19038890-C-T | not specified | Uncertain significance (Jun 04, 2024) | ||
22-19038939-C-T | not specified | Uncertain significance (Dec 02, 2024) | ||
22-19038963-C-T | not specified | Uncertain significance (May 23, 2023) | ||
22-19038984-C-T | not specified | Uncertain significance (Dec 20, 2022) | ||
22-19038985-G-A | Likely benign (Apr 16, 2018) | |||
22-19038993-C-A | not specified | Uncertain significance (Jan 29, 2024) | ||
22-19039043-C-T | Benign (Dec 01, 2023) | |||
22-19039044-G-A | not specified | Uncertain significance (Nov 18, 2022) | ||
22-19039046-C-G | not specified | Uncertain significance (Sep 29, 2023) | ||
22-19039046-C-T | not specified | Uncertain significance (Dec 28, 2023) | ||
22-19039047-G-A | not specified | Uncertain significance (Jul 15, 2021) | ||
22-19039070-C-T | not specified | Uncertain significance (Oct 01, 2024) | ||
22-19039101-C-T | not specified | Uncertain significance (Jun 21, 2022) | ||
22-19039112-G-C | not specified | Uncertain significance (Dec 04, 2023) | ||
22-19039113-C-T | not specified | Uncertain significance (Dec 04, 2023) | ||
22-19041065-G-T | not specified | Uncertain significance (May 01, 2022) | ||
22-19041067-C-A | not specified | Uncertain significance (Aug 12, 2022) | ||
22-19041084-G-A | not specified | Uncertain significance (Aug 28, 2023) | ||
22-19041106-G-T | not specified | Uncertain significance (Mar 16, 2022) | ||
22-19041137-C-T | Benign/Likely benign (May 01, 2023) | |||
22-19041181-G-C | not specified | Uncertain significance (Aug 31, 2023) | ||
22-19041186-G-A | not specified | Uncertain significance (Jun 28, 2024) | ||
22-19041200-G-A | not specified | Likely benign (Sep 04, 2024) | ||
22-19041222-G-A | not specified | Uncertain significance (Apr 17, 2023) | ||
22-19041231-G-A | Uncertain significance (Oct 01, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
DGCR2 | protein_coding | protein_coding | ENST00000263196 | 10 | 86173 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000516 | 0.968 | 125715 | 0 | 33 | 125748 | 0.000131 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.664 | 327 | 363 | 0.902 | 0.0000245 | 3591 |
Missense in Polyphen | 125 | 162.92 | 0.76723 | 1700 | ||
Synonymous | 0.128 | 155 | 157 | 0.987 | 0.0000117 | 1096 |
Loss of Function | 1.98 | 12 | 22.0 | 0.546 | 9.39e-7 | 258 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000397 | 0.000394 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.000555 | 0.000554 |
European (Non-Finnish) | 0.000102 | 0.0000879 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Putative adhesion receptor, that could be involved in cell-cell or cell-matrix interactions required for normal cell differentiation and migration.;
Recessive Scores
- pRec
- 0.267
Intolerance Scores
- loftool
- 0.269
- rvis_EVS
- -1.17
- rvis_percentile_EVS
- 6.03
Haploinsufficiency Scores
- pHI
- 0.260
- hipred
- N
- hipred_score
- 0.241
- ghis
- 0.562
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.566
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dgcr2
- Phenotype
- homeostasis/metabolism phenotype; hematopoietic system phenotype; skeleton phenotype; immune system phenotype;
Gene ontology
- Biological process
- cell adhesion;animal organ morphogenesis;cognition
- Cellular component
- integral component of membrane
- Molecular function
- carbohydrate binding