DGCR6L

DiGeorge syndrome critical region gene 6 like

Basic information

Region (hg38): 22:20314237-20320080

Links

ENSG00000128185 ∙ NCBI:85359 ∙ OMIM:609459 ∙ HGNC:18551 ∙ Uniprot:Q9BY27 ∙ 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 DGCR6L gene.

• Inborn genetic diseases (10 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGCR6L 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				1		1
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in DGCR6L

This is a list of pathogenic ClinVar variants found in the DGCR6L region.

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

Position	Type	Phenotype	Significance	ClinVar
22-20314730-G-A		Malignant tumor of prostate	Uncertain significance (-)
22-20314764-G-A		not specified	Uncertain significance (Aug 08, 2023)
22-20314770-C-T		not specified	Uncertain significance (Nov 06, 2023)
22-20314785-T-G		not specified	Uncertain significance (Jan 03, 2024)
22-20314794-G-A		not specified	Uncertain significance (Sep 16, 2021)
22-20315373-G-A		not specified	Uncertain significance (Nov 09, 2023)
22-20315457-C-T		not specified	Uncertain significance (Jun 30, 2022)
22-20315469-T-C		not specified	Uncertain significance (Feb 28, 2024)
22-20316129-C-T		not specified	Uncertain significance (Jun 23, 2021)
22-20316153-G-A		not specified	Uncertain significance (Mar 17, 2023)
22-20316204-A-G		not specified	Uncertain significance (Apr 25, 2023)
22-20316219-A-G		not specified	Uncertain significance (Dec 11, 2023)
22-20319694-G-A			Benign/Likely benign (Mar 01, 2023)
22-20319747-G-A		not specified	Uncertain significance (Apr 04, 2023)
22-20319755-G-T		not specified	Uncertain significance (Feb 17, 2023)
22-20319962-C-A		not specified	Uncertain significance (May 18, 2023)
22-20319976-C-T		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DGCR6L	protein_coding	protein_coding	ENST00000248879	5	5805

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000506	0.685	125513	0	29	125542	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.535	114	131	0.869	0.00000755	1382
Missense in Polyphen		44	51.504	0.8543		620
Synonymous	0.802	48	55.6	0.863	0.00000296	446
Loss of Function	0.931	8	11.4	0.702	5.72e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000874	0.0000874
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000114	0.000106
Middle Eastern	0.000164	0.000163
South Asian	0.000360	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.673
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.172
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.941

Gene Damage Prediction

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

Gene ontology

• Cellular component: nucleus
• Molecular function: protein binding