DSE

dermatan sulfate epimerase

Basic information

Region (hg38): 6:116254172-116444861

Previous symbols: [ "SART2" ]

Links

ENSG00000111817 ∙ NCBI:29940 ∙ OMIM:605942 ∙ HGNC:21144 ∙ Uniprot:Q9UL01 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Ehlers-Danlos syndrome, musculocontractural type 2 (Limited), mode of inheritance: AR
• Ehlers-Danlos syndrome, musculocontractural type 2 (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, musculocontractural type 2 (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, musculocontractural type 2 (Moderate), mode of inheritance: AR
• Ehlers-Danlos syndrome, musculocontractural type 2 (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, musculocontractural type (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ehlers-Danlos syndrome, musculocontractural type 2	AR	Cardiovascular; Hematologic; Musculoskeletal	Extrapolating from similar types of Ehlers-Danlos syndrome, clinical issues relate to connective tissue fragility may affect multiple organs related to bleeding diatheses (eg, after minor trauma), such that recognition may allow precautions and preventive measures, as well as rapid treatment	Cardiovascular; Craniofacial; Dental; Dermatologic; Gastrointestinal; Hematologic; Musculoskeletal; Neurologic; Ophthalmologic	23704329

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DSE gene.

• Ehlers-Danlos syndrome, musculocontractural type 2 (210 variants)
• not provided (123 variants)
• Inborn genetic diseases (48 variants)
• not specified (23 variants)
• Ehlers-Danlos syndrome (16 variants)
• Sudden infant death-dysgenesis of the testes syndrome (3 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DSE 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				84	2	86
missense			143	5	6	154
nonsense		2	3			5
start loss						0
frameshift	1	2	5			8
inframe indel					1	1
splice donor/acceptor (+/-2bp)		1				1
splice region				2		2
non coding		2	21	31	20	74
Total	1	7	172	120	29

Highest pathogenic variant AF is 0.00000658

Variants in DSE

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

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

Position	Type	Phenotype	Significance	ClinVar
6-116278562-C-T			Likely benign (Jun 08, 2018)
6-116278567-G-A			Likely benign (Oct 13, 2022)
6-116278696-T-C		not specified	Benign (Jan 04, 2024)
6-116278715-G-A			Likely benign (Jul 22, 2021)
6-116278733-G-T		not specified • TSPYL1-related disorder	Likely benign (Jan 22, 2024)
6-116278748-A-G		TSPYL1-related disorder	Likely benign (Jul 12, 2019)
6-116278764-A-G		Inborn genetic diseases	Uncertain significance (Apr 01, 2022)
6-116278772-A-G			Likely benign (Sep 03, 2021)
6-116278911-A-G		Sudden infant death-dysgenesis of the testes syndrome	Uncertain significance (-)
6-116278928-T-C			Likely benign (Dec 19, 2022)
6-116278942-C-A		Inborn genetic diseases	Uncertain significance (Oct 04, 2022)
6-116278948-C-T		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)
6-116279003-C-T			Likely benign (Nov 01, 2022)
6-116279076-T-C		Inborn genetic diseases	Uncertain significance (Jan 16, 2024)
6-116279104-TCA-T		Sudden infant death-dysgenesis of the testes syndrome	Pathogenic/Likely pathogenic (May 14, 2020)
6-116279184-T-G		Inborn genetic diseases	Uncertain significance (Sep 23, 2023)
6-116279191-C-A		Inborn genetic diseases	Uncertain significance (Nov 04, 2022)
6-116279212-C-T		Inborn genetic diseases	Uncertain significance (Jan 09, 2024)
6-116279230-C-T		Inborn genetic diseases	Uncertain significance (Jul 19, 2022)
6-116279246-C-A		Inborn genetic diseases	Uncertain significance (Apr 08, 2022)
6-116279251-C-A			Uncertain significance (Aug 24, 2022)
6-116279256-ACCT-A			Likely benign (Apr 03, 2023)
6-116279265-T-G		Inborn genetic diseases	Uncertain significance (Jun 11, 2021)
6-116279290-C-T			Benign (Jan 29, 2024)
6-116279302-T-TCAC		Ehlers-Danlos syndrome, musculocontractural type 2	Benign (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DSE	protein_coding	protein_coding	ENST00000331677	5	187089

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.633	0.367	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.03	393	523	0.751	0.0000272	6327
Missense in Polyphen		111	194.65	0.57026		2379
Synonymous	1.08	181	201	0.903	0.0000110	1853
Loss of Function	4.54	8	38.3	0.209	0.00000206	422

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000105
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Converts D-glucuronic acid to L-iduronic acid (IdoUA) residues. {ECO:0000269|PubMed:16505484}.
• Pathway: Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human);Metabolism of carbohydrates;Dermatan sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;dermatan sulfate biosynthesis (late stages);Proteoglycan biosynthesis;dermatan sulfate biosynthesis;Metabolism (Consensus)

Recessive Scores

• pRec: 0.150

Intolerance Scores

• loftool: 0.761
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.54

Haploinsufficiency Scores

• pHI: 0.168
• hipred: Y
• hipred_score: 0.554
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.841

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dse
• Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); limbs/digits/tail phenotype; reproductive system phenotype

Gene ontology

• Biological process: heparan sulfate proteoglycan biosynthetic process;chondroitin sulfate biosynthetic process;dermatan sulfate biosynthetic process
• Cellular component: Golgi membrane;nucleoplasm;endoplasmic reticulum;Golgi apparatus;cytosol;integral component of membrane
• Molecular function: chondroitin-glucuronate 5-epimerase activity