DNAJC5
DnaJ heat shock protein family (Hsp40) member C5, the group of MicroRNA protein coding host genes|DNAJ (HSP40) heat shock proteins
Basic information
Region (hg38): 20:63895126-63936031
Previous symbols: [ "CLN4" ]
Links
Phenotypes
GenCC
Source:
- ceroid lipofuscinosis, neuronal, 4 (Kufs type) (Strong), mode of inheritance: AD
- ceroid lipofuscinosis, neuronal, 4 (Kufs type) (Strong), mode of inheritance: AD
- ceroid lipofuscinosis, neuronal, 4 (Kufs type) (Supportive), mode of inheritance: AD
- adult neuronal ceroid lipofuscinosis (Moderate), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Ceroid lipofuscinosis, neuronal, 4 (Kufs type), autosomal dominant | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Biochemical; Neurologic | 5132971; 4414475; 62240; 932739; 11489285; 12112194; 21820099; 22073189; 22235333; 22978711 |
ClinVar
This is a list of variants' phenotypes submitted to
- Neuronal_ceroid_lipofuscinosis (204 variants)
- not_provided (69 variants)
- not_specified (31 variants)
- Ceroid_lipofuscinosis,_neuronal,_4_(Kufs_type) (29 variants)
- Inborn_genetic_diseases (28 variants)
- Neuronal_Ceroid-Lipofuscinosis,_Recessive (12 variants)
- DNAJC5-related_disorder (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNAJC5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000025219.3. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 90 | 93 | ||||
| missense | 82 | 91 | ||||
| nonsense | 2 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | |||||
| Total | 2 | 0 | 88 | 97 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DNAJC5 | protein_coding | protein_coding | ENST00000360864 | 4 | 40867 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.812 | 0.187 | 125279 | 0 | 1 | 125280 | 0.00000399 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.79 | 66 | 122 | 0.543 | 0.00000864 | 1292 |
| Missense in Polyphen | 10 | 37.796 | 0.26458 | 428 | ||
| Synonymous | -1.12 | 70 | 59.0 | 1.19 | 0.00000574 | 361 |
| Loss of Function | 2.62 | 1 | 9.89 | 0.101 | 4.32e-7 | 119 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000617 | 0.0000617 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as a general chaperone in regulated exocytosis (By similarity). Acts as a co-chaperone for the SNARE protein SNAP-25 (By similarity). Involved in the calcium-mediated control of a late stage of exocytosis (By similarity). May have an important role in presynaptic function. May be involved in calcium-dependent neurotransmitter release at nerve endings (By similarity). {ECO:0000250|UniProtKB:P60904, ECO:0000250|UniProtKB:Q29455}.;
- Disease
- DISEASE: Ceroid lipofuscinosis, neuronal, 4B (CLN4B) [MIM:162350]: An adult-onset neuronal ceroid lipofuscinosis. Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterized by intracellular accumulation of autofluorescent liposomal material, and clinically by seizures, dementia, visual loss, and/or cerebral atrophy. CLN4B has no visual involvement and is characterized by seizures and other neurologic symptoms. {ECO:0000269|PubMed:21820099, ECO:0000269|PubMed:22073189, ECO:0000269|PubMed:22235333, ECO:0000269|PubMed:22902780, ECO:0000269|PubMed:22978711}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Protein processing in endoplasmic reticulum - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System;Neuronal System;GABA synthesis, release, reuptake and degradation;Neurotransmitter release cycle;Transmission across Chemical Synapses
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.07
Haploinsufficiency Scores
- pHI
- 0.179
- hipred
- Y
- hipred_score
- 0.765
- ghis
- 0.608
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dnajc5
- Phenotype
- hearing/vestibular/ear 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); vision/eye phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); muscle phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- exocytosis;synaptic vesicle exocytosis;neutrophil degranulation;negative regulation of neuron apoptotic process;regulated exocytosis;chaperone-mediated protein folding;regulation of synaptic vesicle cycle
- Cellular component
- mitochondrion;lysosomal membrane;plasma membrane;membrane;neuromuscular junction;azurophil granule membrane;specific granule membrane;melanosome;clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane;anchored component of synaptic vesicle membrane
- Molecular function
- protein binding;ATP-dependent protein binding