HEXD

protein-coding

hexosaminidase D, the group of Hexosaminidases

Gene summary

Enables beta-N-acetylhexosaminidase activity. Predicted to be involved in carbohydrate metabolic process. Located in extracellular vesicle. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

HEXDC

MANE transcript

NM_001330542.2

Inheritance

—

ClinVar variants

U:103B:20

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr17:82,418,318-82,442,645

External References & Databases

Ensembl (ENSG00000169660)

Transcript & Mutation Effects

hg38 • Region Span ~24.3 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 HEXD variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 123

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001330542.2. 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			17 clinvar	6 clinvar		23
missense			85 clinvar	14 clinvar		99
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	103	20	0	123

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 65 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001330542.2	RefSeq	NP_001317471.1	12	MANE Select
ENST00000327949.15	Ensembl	ENSP00000332634.9	12	MANE Select
NM_001369487.1	RefSeq	NP_001356416.1	11	Standard
NM_001369488.1	RefSeq	NP_001356417.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

carbohydrate metabolic process

Molecular Function

beta-N-acetylhexosaminidase activity
hexosaminidase activity
N-acetyl-beta-D-galactosaminidase activity

Cellular Component

nucleus
cytoplasm
extracellular vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000337014
Coding exons: 11
Length: 24328
Individuals with no LoFs: 124669
Homozygous LoFs: 0
Heterozygous LoFs: 132
Defined: 124801
p: 0.000529

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.565	342	373	0.918	0.0000242	3690
Missense (PolyPhen)		53	68.524	0.77345		747
Synonymous	0.456	163	171	0.956	0.0000123	1265
Loss of Function	1.02	19	24.4	0.777	0.00000113	266

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00079	0.00077	rare
Latino/Admixed American	0.00085	0.00081	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00029	0.00019	rare
European (Non-Finnish)	0.00079	0.00072	rare
South Asian	0.00010	0.000098	rare
Other	0.00019	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Has hexosaminidase activity. {ECO:0000269|PubMed:19040401}.;

Intolerance Scores

RVIS EVS: 0.56
RVIS percentile EVS: 81.71

Essentials

Essential (gene trap): N