DGCR6

DiGeorge syndrome critical region gene 6

Basic information

Region (hg38): 22:18906028-18914238

Links

ENSG00000183628 ∙ NCBI:8214 ∙ OMIM:601279 ∙ HGNC:2846 ∙ Uniprot:Q14129 ∙ 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 DGCR6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGCR6 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				2	1	3
missense			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	19	4	1

Variants in DGCR6

This is a list of pathogenic ClinVar variants found in the DGCR6 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-18906385-A-G		not specified	Uncertain significance (Aug 15, 2023)
22-18906398-G-A			Benign (May 27, 2017)
22-18906402-G-A		not specified	Uncertain significance (Dec 04, 2024)
22-18906414-G-A		not specified	Uncertain significance (Apr 06, 2024)
22-18906439-A-G		not specified	Uncertain significance (Jul 30, 2024)
22-18906446-G-C			Likely benign (Jun 01, 2022)
22-18906468-G-A		not specified	Uncertain significance (May 06, 2022)
22-18906601-C-G		not specified	Uncertain significance (Oct 19, 2024)
22-18906708-T-A		not specified	Uncertain significance (Jan 26, 2023)
22-18910208-C-T		not specified	Uncertain significance (Dec 04, 2024)
22-18910222-C-G		not specified	Uncertain significance (Feb 17, 2024)
22-18910223-G-A		not specified	Uncertain significance (Dec 13, 2023)
22-18910241-T-G		not specified	Uncertain significance (Dec 28, 2023)
22-18910262-G-A		not specified	Uncertain significance (Aug 20, 2024)
22-18910882-C-T			Benign (Feb 01, 2024)
22-18910900-C-G		not specified	Uncertain significance (Mar 31, 2024)
22-18910901-G-A		not specified	Uncertain significance (Feb 06, 2024)
22-18910903-A-C		not specified	Uncertain significance (Oct 12, 2024)
22-18910919-G-A		not specified	Uncertain significance (Aug 28, 2023)
22-18910921-G-A		not specified	Uncertain significance (Mar 24, 2023)
22-18910922-C-T		not specified	Uncertain significance (Jul 19, 2022)
22-18910935-G-A			Likely benign (Jun 01, 2022)
22-18910955-G-A			Likely benign (Jan 01, 2023)
22-18910958-A-G		not specified	Uncertain significance (Oct 29, 2024)
22-18910993-G-A		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DGCR6	protein_coding	protein_coding	ENST00000331444	5	8211

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.82e-12	0.0120	125099	1	160	125260	0.000643

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.138	130	126	1.03	0.00000700	1371
Missense in Polyphen		40	36.072	1.1089		446
Synonymous	-0.739	63	56.0	1.13	0.00000290	448
Loss of Function	-0.877	15	11.8	1.28	5.89e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00712	0.00687
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000161	0.000150
Middle Eastern	0.000168	0.000163
South Asian	0.000306	0.000294
Other	0.000501	0.000491

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in neural crest cell migration into the third and fourth pharyngeal pouches.

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.736
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.1

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.476

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dgcr6

Gene ontology

• Biological process: cell adhesion;animal organ morphogenesis
• Cellular component: nucleus;extracellular matrix
• Molecular function: molecular_function