HDC

histidine decarboxylase

Basic information

Region (hg38): 15:50241947-50265965

Links

ENSG00000140287

∙ NCBI:3067 ∙ OMIM:142704 ∙ HGNC:4855 ∙ Uniprot:P19113 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Tourette syndrome (Limited), mode of inheritance: Unknown
Tourette syndrome (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Tourette's syndrome	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	Neurologic	20445167

ClinVar

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

not_specified (64 variants)
not_provided (7 variants)
Tourette_syndrome (6 variants)
HDC-related_disorder (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDC gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002112.4. 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				6 clinvar	1 clinvar	7
missense			62 clinvar	5 clinvar	1 clinvar	68
nonsense	1 clinvar					1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)	1 clinvar	1 clinvar				2
Total	2	1	63	11	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDC	protein_coding	protein_coding	ENST00000267845	12	24080

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00411	0.996	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	312	368	0.848	0.0000216	4359
Missense in Polyphen		100	158.66	0.63026		1907
Synonymous	-0.849	157	144	1.09	0.00000866	1318
Loss of Function	3.49	10	31.0	0.323	0.00000189	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000173	0.000173
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the biosynthesis of histamine from histidine. {ECO:0000269|PubMed:22767596}.;
Pathway: Histidine metabolism - Homo sapiens (human);Histidine Metabolism;Histidinemia;Amino Acid metabolism;Biogenic Amine Synthesis;Histidine catabolism;Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism;Metabolism of amino acids and derivatives;Metabolism;histamine biosynthesis;Histidine degradation (Consensus)

Recessive Scores

pRec: 0.256

Intolerance Scores

loftool: 0.409
rvis_EVS: -0.24
rvis_percentile_EVS: 36.17

Haploinsufficiency Scores

pHI: 0.191
hipred: Y
hipred_score: 0.554
ghis: 0.400

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.960

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Hdc
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system 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); homeostasis/metabolism phenotype; immune system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;

Zebrafish Information Network

Gene name: hdc
Affected structure: brain
Phenotype tag: abnormal
Phenotype quality: morphology

Gene ontology

Biological process: histamine biosynthetic process;histidine metabolic process;histidine catabolic process;catecholamine biosynthetic process
Cellular component: cytosol
Molecular function: histidine decarboxylase activity;protein binding;pyridoxal phosphate binding