DGCR2

DiGeorge syndrome critical region gene 2, the group of C-type lectin domain containing

Basic information

Region (hg38): 22:19036281-19122454

Links

ENSG00000070413 ∙ NCBI:9993 ∙ OMIM:600594 ∙ HGNC:2845 ∙ Uniprot:P98153 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the DGCR2 gene.

• Inborn genetic diseases (34 variants)
• not provided (10 variants)

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				3	3	6
missense			37		1	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	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
22-19038963-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)
22-19039101-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)
22-19041222-G-A		not specified	Uncertain significance (Apr 17, 2023)
22-19041231-G-A			Uncertain significance (Oct 01, 2023)
22-19041241-C-T		not specified	Uncertain significance (May 11, 2022)
22-19041833-C-T		not specified	Uncertain significance (Jun 09, 2022)
22-19041877-C-T			Likely benign (Apr 10, 2018)
22-19041888-T-C		not specified	Uncertain significance (Jan 29, 2024)
22-19041912-C-T		not specified	Uncertain significance (Sep 21, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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