HDDC2

HD domain containing 2

Basic information

Region (hg38): 6:125219962-125302078

Previous symbols: [ "C6orf74" ]

Links

ENSG00000111906 ∙ NCBI:51020 ∙ ∙ HGNC:21078 ∙ Uniprot:Q7Z4H3 ∙ 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 HDDC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDDC2 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in HDDC2

This is a list of pathogenic ClinVar variants found in the HDDC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-125220143-A-G		not specified	Uncertain significance (Jun 05, 2024)
6-125220147-T-C		not specified	Uncertain significance (Jun 28, 2023)
6-125229180-G-C		not specified	Uncertain significance (Jan 10, 2022)
6-125248344-A-G		not specified	Uncertain significance (Mar 21, 2023)
6-125262846-G-A		not specified	Uncertain significance (Sep 29, 2023)
6-125262850-C-T		not specified	Uncertain significance (Mar 21, 2023)
6-125262873-G-A		not specified	Uncertain significance (Dec 03, 2024)
6-125262882-C-G		not specified	Uncertain significance (Nov 12, 2021)
6-125262951-C-G		not specified	Uncertain significance (Jun 12, 2023)
6-125276184-T-C		not specified	Likely benign (Oct 07, 2024)
6-125276219-A-G		not specified	Uncertain significance (Nov 01, 2022)
6-125276234-T-C		not specified	Likely benign (Feb 28, 2024)
6-125277107-G-A		not specified	Uncertain significance (Aug 09, 2021)
6-125277116-T-C		not specified	Uncertain significance (Jun 11, 2021)
6-125277126-G-T		not specified	Uncertain significance (Apr 17, 2023)
6-125277236-T-C		not specified	Uncertain significance (Dec 22, 2023)
6-125292854-T-C		not specified	Uncertain significance (Nov 21, 2023)
6-125292903-T-C		not specified	Uncertain significance (Nov 11, 2024)
6-125298727-T-C		not specified	Uncertain significance (May 04, 2023)
6-125298751-T-A		not specified	Uncertain significance (Dec 14, 2023)
6-125298808-C-T		not specified	Uncertain significance (Jul 09, 2024)
6-125298809-G-A		not specified	Uncertain significance (Dec 13, 2023)
6-125300546-G-T		not specified	Uncertain significance (Sep 27, 2021)
6-125300562-T-C		not specified	Uncertain significance (Oct 25, 2022)
6-125300572-T-C		not specified	Uncertain significance (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDDC2	protein_coding	protein_coding	ENST00000398153	6	82175

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000203	0.727	124768	0	26	124794	0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0891	112	115	0.977	0.00000602	1331
Missense in Polyphen		41	34.977	1.1722		392
Synonymous	0.364	38	41.0	0.928	0.00000212	385
Loss of Function	1.07	9	13.2	0.682	8.28e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000456	0.000456
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.0000974	0.0000971
Middle Eastern	0.00	0.00
South Asian	0.0000338	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.610
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.0893
• hipred: N
• hipred_score: 0.394
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.257

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hddc2

Gene ontology

• Biological process: dUMP biosynthetic process;pyrimidine deoxyribonucleotide salvage;dephosphorylation
• Molecular function: 5'-deoxynucleotidase activity;protein binding