HEXD

hexosaminidase D, the group of Hexosaminidases

Basic information

Region (hg38): 17:82418317-82442645

Previous symbols: [ "HEXDC" ]

Links

ENSG00000169660 ∙ NCBI:284004 ∙ OMIM:616864 ∙ HGNC:26307 ∙ Uniprot:Q8WVB3 ∙ 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 HEXD gene.

• Inborn genetic diseases (9 variants)
• not specified (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HEXD 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					1	1
missense			6	4	1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	6	4	3

Variants in HEXD

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

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

Position	Type	Phenotype	Significance	ClinVar
17-82418479-G-A		not specified	Uncertain significance (Jan 23, 2024)
17-82419814-T-G		not specified	Benign (Mar 29, 2016)
17-82419872-T-C		not specified	Uncertain significance (Oct 02, 2023)
17-82424443-A-T		not specified	Uncertain significance (Aug 08, 2023)
17-82428642-G-A		not specified	Uncertain significance (Jun 30, 2022)
17-82433674-C-T		not specified	Uncertain significance (Sep 29, 2022)
17-82433682-G-A		not specified	Uncertain significance (Jun 21, 2022)
17-82433730-G-A		not specified	Likely benign (Oct 13, 2023)
17-82433782-T-C		not specified	Uncertain significance (Jan 19, 2024)
17-82433794-C-G		not specified	Uncertain significance (Feb 22, 2023)
17-82433800-G-A		not specified	Uncertain significance (Feb 13, 2024)
17-82433808-A-G		not specified	Benign (Mar 29, 2016)
17-82433811-G-A		not specified	Uncertain significance (Jan 20, 2023)
17-82435751-G-A		not specified	Likely benign (Feb 27, 2024)
17-82435752-G-A		not specified	Uncertain significance (May 16, 2022)
17-82435768-C-T		not specified	Uncertain significance (Jan 31, 2024)
17-82435771-A-C		not specified	Uncertain significance (Jun 29, 2022)
17-82435777-G-A		not specified	Uncertain significance (Jan 18, 2022)
17-82435791-G-A		not specified	Uncertain significance (Apr 07, 2022)
17-82435794-G-A		not specified	Uncertain significance (Apr 07, 2022)
17-82435807-G-A		not specified	Likely benign (Oct 25, 2023)
17-82435850-C-A		not specified	Uncertain significance (Jun 09, 2022)
17-82436654-G-T		not specified	Benign (Mar 29, 2016)
17-82436690-G-A		not specified	Uncertain significance (Aug 12, 2021)
17-82436699-C-G		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HEXD	protein_coding	protein_coding	ENST00000337014	11	24328

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.34e-11	0.336	124669	0	132	124801	0.000529

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.565	342	373	0.918	0.0000242	3690
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00164	0.00163
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000111
Finnish	0.000294	0.000186
European (Non-Finnish)	0.000786	0.000724
Middle Eastern	0.000112	0.000111
South Asian	0.000104	0.0000980
Other	0.000191	0.000165

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• rvis_EVS: 0.56
• rvis_percentile_EVS: 81.71

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.123
• ghis: 0.434

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Hexdc

Gene ontology

• Biological process: carbohydrate metabolic process
• Cellular component: nucleus;cytoplasm;extracellular vesicle
• Molecular function: beta-N-acetylhexosaminidase activity;hexosaminidase activity;N-acetyl-beta-D-galactosaminidase activity