DGLUCY

D-glutamate cyclase, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 14:91060333-91225632

Previous symbols: [ "C14orf159" ]

Links

ENSG00000133943 ∙ NCBI:80017 ∙ ∙ HGNC:20498 ∙ Uniprot:Q7Z3D6 ∙ 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 DGLUCY gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGLUCY 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						0
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in DGLUCY

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

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

Position	Type	Phenotype	Significance	ClinVar
14-91060343-T-A		not specified	Uncertain significance (Nov 23, 2021)
14-91060373-C-A		not specified	Uncertain significance (Mar 02, 2023)
14-91060379-C-A		not specified	Uncertain significance (Apr 25, 2023)
14-91060383-C-G		not specified	Uncertain significance (Jun 23, 2023)
14-91060385-T-C		not specified	Uncertain significance (Sep 17, 2021)
14-91060413-T-G		not specified	Uncertain significance (Nov 01, 2022)
14-91188915-C-T		not specified	Uncertain significance (Aug 23, 2021)
14-91189125-G-A		not specified	Uncertain significance (Aug 23, 2021)
14-91196438-C-T		not specified	Uncertain significance (Aug 25, 2021)
14-91199788-G-A		not specified	Uncertain significance (Jun 18, 2021)
14-91224732-G-A		not specified	Uncertain significance (Aug 09, 2021)
14-91224778-A-G		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DGLUCY	protein_coding	protein_coding	ENST00000518868	12	165300

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.66e-22	0.000194	125624	1	122	125747	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.817	404	360	1.12	0.0000194	4007
Missense in Polyphen		81	82.332	0.98382		1109
Synonymous	-1.15	174	156	1.12	0.00000986	1290
Loss of Function	-0.713	31	27.0	1.15	0.00000123	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00207	0.00206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000780	0.000761
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000401	0.000396
Middle Eastern	0.000780	0.000761
South Asian	0.000592	0.000523
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: D-glutamate cyclase that converts D-glutamate to 5-oxo- D-proline. {ECO:0000250|UniProtKB:Q8BH86}.
• Pathway: D-Glutamine and D-glutamate metabolism - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0904

Intolerance Scores

• rvis_EVS: 1.89
• rvis_percentile_EVS: 97.33

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.161

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Dglucy
• Phenotype: homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: glutamate metabolic process;biological_process
• Cellular component: cellular_component;mitochondrial matrix
• Molecular function: molecular_function;protein binding;D-glutamate cyclase activity