YDJC

YdjC chitooligosaccharide deacetylase homolog

Basic information

Region (hg38): 22:21628089-21630064

Links

ENSG00000161179 ∙ NCBI:150223 ∙ OMIM:619770 ∙ HGNC:27158 ∙ Uniprot:A8MPS7 ∙ 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 YDJC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YDJC 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in YDJC

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

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

Position	Type	Phenotype	Significance	ClinVar
22-21628437-A-T		not specified	Uncertain significance (Jul 11, 2023)
22-21628512-A-T		not specified	Uncertain significance (Feb 12, 2024)
22-21628566-C-T		not specified	Uncertain significance (Jul 21, 2021)
22-21628573-C-T		not specified	Uncertain significance (Aug 31, 2022)
22-21628582-G-A		not specified	Uncertain significance (Nov 13, 2024)
22-21628608-G-A		not specified	Uncertain significance (Dec 15, 2023)
22-21628609-G-A		not specified	Uncertain significance (Mar 19, 2024)
22-21628635-G-C		not specified	Uncertain significance (Feb 16, 2023)
22-21628641-C-A		not specified	Uncertain significance (Apr 08, 2024)
22-21628699-C-T		not specified	Uncertain significance (Aug 02, 2023)
22-21628713-G-A		not specified	Uncertain significance (Oct 06, 2024)
22-21628737-G-A		not specified	Uncertain significance (Feb 01, 2023)
22-21628749-C-A		not specified	Uncertain significance (May 09, 2023)
22-21629020-G-A		not specified	Uncertain significance (Jan 04, 2022)
22-21629023-G-A		not specified	Uncertain significance (Aug 04, 2023)
22-21629047-G-A		not specified	Uncertain significance (Mar 06, 2023)
22-21629082-G-A		not specified	Uncertain significance (Aug 19, 2024)
22-21629113-C-T		not specified	Uncertain significance (Mar 29, 2023)
22-21629142-C-G		not specified	Uncertain significance (Feb 28, 2024)
22-21629187-C-A		not specified	Uncertain significance (Aug 31, 2022)
22-21629358-C-A		not specified	Uncertain significance (May 17, 2023)
22-21629637-C-T		not specified	Uncertain significance (Mar 07, 2023)
22-21629640-G-A		not specified	Uncertain significance (Feb 15, 2023)
22-21629696-C-A		not specified	Uncertain significance (Apr 26, 2023)
22-21629700-G-A		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YDJC	protein_coding	protein_coding	ENST00000292778	5	1976

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0624	0.876	124218	0	35	124253	0.000141

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	146	202	0.721	0.0000128	1992
Missense in Polyphen		47	63.613	0.73884		693
Synonymous	2.11	69	95.1	0.725	0.00000660	726
Loss of Function	1.57	3	7.71	0.389	3.67e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00128	0.00125
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000145	0.000117
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000168	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably catalyzes the deacetylation of acetylated carbohydrates an important step in the degradation of oligosaccharides. {ECO:0000250|UniProtKB:Q53WD3}.

Recessive Scores

• pRec: 0.102

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.354
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ydjc
• Phenotype: vision/eye phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; growth/size/body region phenotype; pigmentation phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: carbohydrate metabolic process
• Molecular function: magnesium ion binding;hydrolase activity