DNAJC12

DnaJ heat shock protein family (Hsp40) member C12, the group of DNAJ (HSP40) heat shock proteins

Basic information

Region (hg38): 10:67796669-67838188

Links

ENSG00000108176 ∙ NCBI:56521 ∙ OMIM:606060 ∙ HGNC:28908 ∙ Uniprot:Q9UKB3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hyperphenylalaninemia due to DNAJC12 deficiency (Strong), mode of inheritance: AR
• hyperphenylalaninemia due to DNAJC12 deficiency (Supportive), mode of inheritance: AR
• hyperphenylalaninemia due to DNAJC12 deficiency (Definitive), mode of inheritance: AR
• hyperphenylalaninemia due to DNAJC12 deficiency (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hyperphenylalaninemia, mild, non-BH4-deficient	AR	Biochemical	The condition can involve variable neurocognitive dysfunction, and individuals have been reported as benefiting from neurotrnsmitter precursors, especially if initiated in infancy	Biochemical	28132689; 28794131; 29174366; 30139987

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DNAJC12 gene.

• not_provided (86 variants)
• Inborn_genetic_diseases (23 variants)
• Hyperphenylalaninemia_due_to_DNAJC12_deficiency (18 variants)
• DNAJC12-related_disorder (5 variants)
• not_specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNAJC12 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021800.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	11	2	14
missense	2		42	2	2	48
nonsense	4	1				5
start loss		1				1
frameshift	3	2				5
splice donor/acceptor (+/-2bp)	8	1				9
Total	17	5	43	13	4

Highest pathogenic variant AF is 0.0000972945

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNAJC12	protein_coding	protein_coding	ENST00000225171	5	41498

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000207	0.477	125681	0	65	125746	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0635	104	106	0.983	0.00000560	1298
Missense in Polyphen		28	28.689	0.97597		385
Synonymous	0.0825	37	37.6	0.983	0.00000195	339
Loss of Function	0.686	10	12.6	0.792	6.85e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00105	0.00105
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000982	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Hyperphenylalaninemia, mild, non-BH4-deficient (HPANBH4) [MIM:617384]: An autosomal recessive disorder characterized by increased serum phenylalanine, normal BH4 metabolism, and highly variable neurologic defects, including movement abnormalities and intellectual disability. {ECO:0000269|PubMed:28132689}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0954

Intolerance Scores

• loftool: 0.898
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.169
• hipred: N
• hipred_score: 0.216
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.270

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnajc12

Gene ontology

• Cellular component: cytoplasm
• Molecular function: protein binding