YDJC

protein-coding

YdjC chitooligosaccharide deacetylase homolog

Gene summary

Predicted to enable deacetylase activity and magnesium ion binding activity. Predicted to be involved in carbohydrate metabolic process. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001017964.2

Inheritance

—

ClinVar variants

U:50

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr22:21,628,089-21,630,064

External References & Databases

Ensembl (ENSG00000161179)

Transcript & Mutation Effects

hg38 • Region Span ~2.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to YDJC variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 46

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001017964.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			48 clinvar			48
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	50	0	0	50

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001017964.2	RefSeq	NP_001017964.1	5	MANE Select
ENST00000292778.11	Ensembl	ENSP00000292778.6	5	MANE Select
NM_001371350.1	RefSeq	NP_001358279.1	4	Standard
ENST00000398873.4	Ensembl	ENSP00000381847.3	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

carbohydrate metabolic process

Molecular Function

magnesium ion binding
hydrolase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000292778
Coding exons: 5
Length: 1976
Individuals with no LoFs: 124218
Homozygous LoFs: 0
Heterozygous LoFs: 35
Defined: 124253
p: 0.000141

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.41	146	202	0.721	0.0000128	1992
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00035	0.00032	rare
Latino/Admixed American	0.00093	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.00012	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

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