GTDC1

glycosyltransferase like domain containing 1, the group of Glycosyl transferases group 1 domain containing

Basic information

Region (hg38): 2:143938068-144332568

Links

ENSG00000121964 ∙ NCBI:79712 ∙ OMIM:610165 ∙ HGNC:20887 ∙ Uniprot:Q4AE62 ∙ 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 GTDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTDC1 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	2
missense			16	1	1	18
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	2

Variants in GTDC1

This is a list of pathogenic ClinVar variants found in the GTDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-143947121-C-A			Benign (Dec 14, 2017)
2-143947121-C-T			Likely benign (Feb 01, 2023)
2-143947122-G-A			Likely benign (Mar 29, 2018)
2-143947125-G-A		not specified	Uncertain significance (Apr 01, 2024)
2-143947126-C-T		not specified	Likely benign (Apr 01, 2024)
2-143952073-G-A		not specified	Uncertain significance (Jun 27, 2022)
2-143952775-G-C		not specified	Uncertain significance (Dec 06, 2022)
2-143952779-A-G		not specified	Uncertain significance (Oct 20, 2021)
2-143952796-A-C		not specified	Uncertain significance (May 18, 2023)
2-143952808-C-G		not specified	Uncertain significance (Dec 13, 2022)
2-143970676-C-A		not specified	Uncertain significance (Nov 08, 2022)
2-143970733-A-G		not specified	Uncertain significance (Jan 30, 2024)
2-144007245-C-T		not specified	Uncertain significance (Oct 05, 2022)
2-144007291-T-C		not specified	Uncertain significance (Aug 23, 2021)
2-144007477-C-T		not specified	Uncertain significance (Mar 28, 2024)
2-144141907-G-C		not specified	Uncertain significance (Jun 02, 2024)
2-144141915-A-G			Benign (Mar 29, 2018)
2-144141934-T-C		not specified	Uncertain significance (Dec 14, 2022)
2-144141942-C-T		not specified	Uncertain significance (Aug 02, 2021)
2-144141967-C-T		not specified	Uncertain significance (Nov 19, 2022)
2-144142014-A-G		not specified	Uncertain significance (Jul 09, 2021)
2-144142032-A-C		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
2-144208655-G-A		not specified	Uncertain significance (Jul 20, 2022)
2-144208655-G-C		not specified	Uncertain significance (Dec 13, 2023)
2-144208696-A-T		not specified	Uncertain significance (Jan 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTDC1	protein_coding	protein_coding	ENST00000392869	9	394501

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-12	0.0808	125609	1	137	125747	0.000549

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.150	242	236	1.03	0.0000112	3005
Missense in Polyphen		104	106.87	0.97313		1417
Synonymous	0.754	79	88.0	0.898	0.00000457	843
Loss of Function	0.510	20	22.6	0.884	0.00000105	306

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000893	0.000890
Ashkenazi Jewish	0.00	0.00
East Asian	0.000708	0.000707
Finnish	0.0000951	0.0000924
European (Non-Finnish)	0.000537	0.000528
Middle Eastern	0.000708	0.000707
South Asian	0.00101	0.00101
Other	0.00115	0.000978

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0749

Intolerance Scores

• loftool: 0.973
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.56

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.250
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.137

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtdc1

Zebrafish Information Network

• Gene name: gtdc1
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: curved

Gene ontology

• Molecular function: transferase activity, transferring glycosyl groups