DGCR6L

DiGeorge syndrome critical region gene 6 like

Basic information

Region (hg38): 22:20314238-20320080

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.

• not_specified (32 variants)
• not_provided (1 variants)
• Prostate_cancer (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. These statistics are base on transcript: NM_000033257.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			31	2		33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	3	0

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