HDDC3

HD domain containing 3

Basic information

Region (hg38): 15:90929968-90935196

Links

ENSG00000184508 ∙ NCBI:374659 ∙ ∙ HGNC:30522 ∙ Uniprot:Q8N4P3 ∙ 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 HDDC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDDC3 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			8			8
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in HDDC3

This is a list of pathogenic ClinVar variants found in the HDDC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-90931401-C-T			Likely benign (Oct 01, 2023)
15-90931710-G-C		not specified	Uncertain significance (Nov 09, 2024)
15-90931719-G-T		not specified	Uncertain significance (Oct 05, 2023)
15-90931721-T-C		not specified	Uncertain significance (Dec 07, 2023)
15-90931773-C-T		not specified	Uncertain significance (Dec 06, 2024)
15-90931781-C-T		not specified	Uncertain significance (Feb 14, 2023)
15-90931823-T-C		not specified	Uncertain significance (Jun 16, 2024)
15-90932465-C-A		not specified	Uncertain significance (Oct 20, 2024)
15-90932494-G-A		not specified	Uncertain significance (Nov 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDDC3	protein_coding	protein_coding	ENST00000330334	4	1652

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0193	0.752	125679	0	69	125748	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.387	58	66.9	0.867	0.00000303	887
Missense in Polyphen		17	22.309	0.76204		322
Synonymous	0.947	24	30.7	0.782	0.00000148	300
Loss of Function	0.823	3	4.98	0.602	2.13e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00227	0.00227
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000220	0.000220
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ppGpp hydrolyzing enzyme involved in starvation response. {ECO:0000269|PubMed:20818390}.
• Pathway: Purine metabolism - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.575
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.339
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.521

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hddc3
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Molecular function: protein binding;guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity;metal ion binding