HDHD3

haloacid dehalogenase like hydrolase domain containing 3, the group of Haloacid dehalogenase like hydrolase domain containing

Basic information

Region (hg38): 9:113373419-113376986

Previous symbols: [ "C9orf158" ]

Links

ENSG00000119431 ∙ NCBI:81932 ∙ ∙ HGNC:28171 ∙ Uniprot:Q9BSH5 ∙ 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 HDHD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDHD3 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in HDHD3

This is a list of pathogenic ClinVar variants found in the HDHD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-113373634-G-A		not specified	Uncertain significance (Mar 23, 2022)
9-113373672-T-C		not specified	Uncertain significance (Jun 24, 2022)
9-113373751-G-A		not specified	Uncertain significance (Nov 03, 2022)
9-113373784-C-T		not specified	Uncertain significance (Aug 22, 2023)
9-113373786-A-T		not specified	Uncertain significance (Dec 23, 2024)
9-113373843-C-T		not specified	Uncertain significance (Sep 02, 2024)
9-113373850-C-T		not specified	Uncertain significance (Mar 29, 2024)
9-113373859-G-A		not specified	Uncertain significance (Jan 24, 2024)
9-113373887-A-C		not specified	Uncertain significance (Oct 21, 2024)
9-113373893-G-C		not specified	Uncertain significance (Jan 16, 2024)
9-113373919-C-T		not specified	Uncertain significance (Feb 23, 2023)
9-113373975-C-T		not specified	Uncertain significance (Aug 28, 2023)
9-113373976-G-A		not specified	Uncertain significance (Feb 28, 2023)
9-113373988-C-T		not specified	Uncertain significance (Mar 05, 2024)
9-113373994-G-C		not specified	Uncertain significance (Mar 10, 2025)
9-113374026-G-C		not specified	Uncertain significance (Dec 31, 2024)
9-113374069-G-A		not specified	Uncertain significance (Jan 31, 2022)
9-113374123-C-A		not specified	Uncertain significance (Mar 08, 2024)
9-113374140-C-T		not specified	Uncertain significance (Sep 25, 2024)
9-113374161-A-C		not specified	Uncertain significance (Sep 12, 2023)
9-113374165-C-T		not specified	Uncertain significance (May 15, 2024)
9-113374249-G-C		not specified	Uncertain significance (Aug 28, 2024)
9-113374258-C-T		not specified	Uncertain significance (Apr 20, 2023)
9-113374309-C-T		not specified	Uncertain significance (Mar 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDHD3	protein_coding	protein_coding	ENST00000238379	1	3581

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00187	0.741	125682	0	63	125745	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.201	145	152	0.954	0.00000946	1594
Missense in Polyphen		60	50.852	1.1799		540
Synonymous	-0.0810	66	65.2	1.01	0.00000367	565
Loss of Function	0.876	5	7.61	0.657	5.01e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000246	0.000242
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000381	0.000381
Finnish	0.00132	0.00129
European (Non-Finnish)	0.000162	0.000158
Middle Eastern	0.000381	0.000381
South Asian	0.0000980	0.0000980
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0988

Intolerance Scores

• loftool: 0.698
• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.0778
• hipred: N
• hipred_score: 0.219
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.865

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hdhd3

Gene ontology

• Molecular function: protein binding;hydrolase activity