HDHD3

protein-coding

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

Gene summary

Predicted to enable hydrolase activity. Located in nucleolus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C9orf158

MANE transcript

NM_001304509.2

Inheritance

—

ClinVar variants

U:46B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr9:113,373,419-113,376,986

External References & Databases

Ensembl (ENSG00000119431)

Transcript & Mutation Effects

hg38 • Region Span ~3.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HDHD3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 47

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001304509.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			46 clinvar	1 clinvar		47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	1	0	47

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001304509.2	RefSeq	NP_001291438.1	1	MANE Select
ENST00000374180.4	Ensembl	ENSP00000363295.3	1	MANE Select
NM_001304510.2	RefSeq	NP_001291439.1	1	Standard
NM_001304511.2	RefSeq	NP_001291440.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
hydrolase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000238379
Coding exons: 1
Length: 3581
Individuals with no LoFs: 125682
Homozygous LoFs: 0
Heterozygous LoFs: 63
Defined: 125745
p: 0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.201	145	152	0.954	0.00000946	1594
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00038	0.00038	rare
Finnish	0.0013	0.0013	notable
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.000098	0.000098	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0988

Intolerance Scores

LoFtool: 0.698
RVIS EVS: -0.12
RVIS percentile EVS: 45.13

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.865

Gene Damage Prediction

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