GMDS

GDP-mannose 4,6-dehydratase, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 6:1623806-2245605

Links

ENSG00000112699 ∙ NCBI:2762 ∙ OMIM:602884 ∙ HGNC:4369 ∙ Uniprot:O60547 ∙ 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 GMDS gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GMDS 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in GMDS

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

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

Position	Type	Phenotype	Significance	ClinVar
6-1624190-C-T		not specified	Uncertain significance (Nov 06, 2023)
6-1624201-C-T		not specified	Uncertain significance (Jan 17, 2024)
6-1726451-T-C		not specified	Uncertain significance (Jun 17, 2024)
6-1742484-T-C		not specified	Uncertain significance (Mar 07, 2023)
6-1742554-C-T			Likely benign (Dec 01, 2022)
6-1742555-G-A		not specified	Uncertain significance (May 27, 2022)
6-1930219-C-T		not specified	Uncertain significance (Jun 07, 2024)
6-1959956-T-C		not specified	Uncertain significance (Feb 16, 2023)
6-1960870-C-T		not specified	Uncertain significance (Mar 29, 2024)
6-1960923-A-G		not specified	Uncertain significance (Mar 14, 2023)
6-1960938-G-A		not specified	Uncertain significance (Oct 05, 2023)
6-1960950-G-A		not specified	Uncertain significance (Aug 15, 2023)
6-2117477-A-G		not specified	Uncertain significance (Sep 20, 2023)
6-2117538-G-A		not specified	Uncertain significance (Feb 02, 2022)
6-2117541-G-A		not specified	Uncertain significance (Jun 24, 2022)
6-2245374-C-T		not specified	Uncertain significance (Apr 01, 2024)
6-2245397-G-A		not specified	Uncertain significance (Jan 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GMDS	protein_coding	protein_coding	ENST00000380815	11	621886

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.991	0.00868	125736	0	10	125746	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	140	215	0.651	0.0000120	2418
Missense in Polyphen		57	107.6	0.52973		1127
Synonymous	0.963	73	84.2	0.867	0.00000509	702
Loss of Function	4.06	2	23.0	0.0868	0.00000131	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the conversion of GDP-D-mannose to GDP-4- dehydro-6-deoxy-D-mannose.
• Pathway: Fructose and mannose metabolism - Homo sapiens (human);Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Fructose intolerance, hereditary;Fructose and Mannose Degradation;Fructosuria;Fructose Mannose metabolism;Post-translational protein modification;Metabolism of proteins;GDP-fucose biosynthesis;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation;GDP-L-fucose biosynthesis I (from GDP-D-mannose) (Consensus)

Recessive Scores

• pRec: 0.229

Intolerance Scores

• loftool: 0.198
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.203
• hipred: Y
• hipred_score: 0.774
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.940

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gmds
• Phenotype: hematopoietic system phenotype; skeleton phenotype; immune system phenotype; homeostasis/metabolism phenotype; craniofacial phenotype

Zebrafish Information Network

• Gene name: gmds
• Affected structure: secondary motor neuron
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: Notch signaling pathway;GDP-mannose metabolic process;'de novo' GDP-L-fucose biosynthetic process
• Cellular component: cytoplasm;cytosol;extracellular exosome
• Molecular function: protein binding;GDP-mannose 4,6-dehydratase activity;identical protein binding;NADP+ binding