HDHD5

protein-coding

haloacid dehalogenase like hydrolase domain containing 5, the group of Haloacid dehalogenase like hydrolase domain containing

Gene summary

Predicted to be involved in glycerophospholipid biosynthetic process. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CECR5

MANE transcript

NM_033070.3

Inheritance

—

ClinVar variants

U:87B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr22:17,137,511-17,165,287

External References & Databases

Ensembl (ENSG00000069998)

Transcript & Mutation Effects

hg38 • Region Span ~27.8 kb

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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 HDHD5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 90

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033070.3. 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				1 clinvar		1
missense			84 clinvar	9 clinvar	2 clinvar	95
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	87	10	2	99

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033070.3	RefSeq	NP_149061.1	8	MANE Select
ENST00000336737.8	Ensembl	ENSP00000337358.4	8	MANE Select
NM_017829.6	RefSeq	NP_060299.4	8	Standard
ENST00000155674.9	Ensembl	ENSP00000155674.5	8	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000336737
Coding exons: 8
Length: 27777
Individuals with no LoFs: 125687
Homozygous LoFs: 0
Heterozygous LoFs: 61
Defined: 125748
p: 0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.183	233	241	0.967	0.0000146	2689
Missense (PolyPhen)		52	60.726	0.85631		644
Synonymous	-0.228	110	107	1.03	0.00000693	898
Loss of Function	0.513	15	17.3	0.867	9.96e-7	175

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0.00060	0.00060	rare
East Asian	0.00027	0.00027	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00023	0.00023	rare
South Asian	0.00026	0.00026	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0941

Intolerance Scores

RVIS EVS: -0.02
RVIS percentile EVS: 52.09

Essentials

Essential (gene trap): N