HDHD2

haloacid dehalogenase like hydrolase domain containing 2, the group of Haloacid dehalogenase like hydrolase domain containing

Basic information

Region (hg38): 18:47107408-47150500

Links

ENSG00000167220 ∙ NCBI:84064 ∙ ∙ HGNC:25364 ∙ Uniprot:Q9H0R4 ∙ 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 HDHD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDHD2 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in HDHD2

This is a list of pathogenic ClinVar variants found in the HDHD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-47108719-G-A		not specified	Uncertain significance (Jul 10, 2024)
18-47108735-T-C		not specified	Uncertain significance (Apr 22, 2024)
18-47115137-C-T		not specified	Uncertain significance (Jul 12, 2023)
18-47115143-T-A		not specified	Uncertain significance (Nov 24, 2024)
18-47115176-G-A		not specified	Uncertain significance (Oct 01, 2024)
18-47115196-G-T		not specified	Uncertain significance (Jun 01, 2023)
18-47115215-C-T		not specified	Uncertain significance (Sep 16, 2021)
18-47115218-C-T		not specified	Uncertain significance (Mar 07, 2024)
18-47115242-A-G		not specified	Uncertain significance (Oct 29, 2021)
18-47115246-T-G		not specified	Uncertain significance (Nov 08, 2024)
18-47115284-C-T		not specified	Uncertain significance (Sep 29, 2023)
18-47130245-G-A		not specified	Uncertain significance (Jun 24, 2022)
18-47130253-T-G		not specified	Uncertain significance (Nov 25, 2024)
18-47130295-A-G		not specified	Uncertain significance (Dec 06, 2021)
18-47130304-G-A		not specified	Uncertain significance (Dec 06, 2022)
18-47134502-A-T		not specified	Uncertain significance (May 15, 2024)
18-47134588-A-G		not specified	Uncertain significance (May 31, 2022)
18-47134630-C-T		not specified	Uncertain significance (Apr 04, 2023)
18-47134663-G-T		not specified	Uncertain significance (May 15, 2024)
18-47134683-G-C		not specified	Likely benign (Jul 22, 2024)
18-47136382-T-C		not specified	Uncertain significance (Oct 25, 2022)
18-47136402-T-A		not specified	Uncertain significance (Aug 08, 2022)
18-47136426-C-T		not specified	Uncertain significance (Nov 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDHD2	protein_coding	protein_coding	ENST00000300605	6	43118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000387	0.383	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.397	129	142	0.906	0.00000725	1674
Missense in Polyphen		41	50.159	0.8174		596
Synonymous	0.196	51	52.8	0.966	0.00000258	523
Loss of Function	0.424	9	10.5	0.859	5.00e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000150	0.000150
Ashkenazi Jewish	0.000893	0.000893
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000196	0.000193
Middle Eastern	0.00	0.00
South Asian	0.0000673	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0862

Intolerance Scores

• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.0807
• hipred: N
• hipred_score: 0.197
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0208

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hdhd2
• 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)

Gene ontology

• Biological process: biological_process;dephosphorylation
• Cellular component: extracellular exosome
• Molecular function: protein binding;phosphatase activity;enzyme binding;metal ion binding