TMTC1

transmembrane O-mannosyltransferase targeting cadherins 1, the group of Tetratricopeptide repeat domain containing|Transmembrane and tetratricopeptide repeat containing

Basic information

Region (hg38): 12:29500839-29784759

Links

ENSG00000133687 ∙ NCBI:83857 ∙ OMIM:615855 ∙ HGNC:24099 ∙ Uniprot:Q8IUR5 ∙ 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 TMTC1 gene.

• Inborn genetic diseases (42 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMTC1 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				2	2	4
missense			39	3		42
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	39	5	3

Variants in TMTC1

This is a list of pathogenic ClinVar variants found in the TMTC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-29506965-C-T		not specified	Uncertain significance (Nov 03, 2022)
12-29514496-C-T		not specified	Uncertain significance (Mar 29, 2023)
12-29514564-T-C		not specified	Uncertain significance (Jan 19, 2022)
12-29516356-T-C		not specified	Uncertain significance (Sep 14, 2023)
12-29516357-G-A		not specified	Uncertain significance (Dec 19, 2022)
12-29516393-G-A		not specified	Uncertain significance (Oct 29, 2021)
12-29516429-T-A		not specified	Uncertain significance (Feb 03, 2022)
12-29516461-T-C		not specified	Uncertain significance (Jan 10, 2023)
12-29516471-C-T		not specified	Uncertain significance (Feb 05, 2024)
12-29517437-C-T		not specified	Uncertain significance (Jun 29, 2022)
12-29517476-T-C		not specified	Likely benign (Jul 27, 2022)
12-29517511-G-T		not specified	Uncertain significance (Dec 17, 2023)
12-29517561-C-T		not specified	Uncertain significance (Sep 28, 2021)
12-29518473-G-A		not specified	Uncertain significance (Dec 19, 2022)
12-29520716-C-T		not specified	Uncertain significance (Jul 17, 2023)
12-29536226-A-G		not specified	Uncertain significance (Dec 26, 2023)
12-29556990-G-A		not specified	Uncertain significance (Oct 30, 2023)
12-29572132-G-A		not specified	Uncertain significance (Oct 12, 2022)
12-29572145-G-A		not specified	Uncertain significance (Dec 15, 2022)
12-29572150-T-C		not specified	Uncertain significance (Jan 09, 2024)
12-29572192-T-C		not specified	Uncertain significance (Aug 21, 2023)
12-29583398-T-C			Benign (May 14, 2018)
12-29604202-G-A		not specified	Uncertain significance (Apr 25, 2022)
12-29604242-G-C		not specified	Uncertain significance (Jan 31, 2024)
12-29604282-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMTC1	protein_coding	protein_coding	ENST00000539277	18	283920

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.33e-9	0.999	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.711	409	452	0.906	0.0000240	5674
Missense in Polyphen		132	175.19	0.75346		2062
Synonymous	-0.671	188	177	1.06	0.00000968	1737
Loss of Function	3.06	22	43.9	0.501	0.00000221	543

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000744	0.000744
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.000381	0.000381
South Asian	0.000165	0.000163
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.785
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.79

Haploinsufficiency Scores

• pHI: 0.330
• hipred: Y
• hipred_score: 0.554
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.367

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmtc1

Gene ontology

• Biological process: RNA processing
• Cellular component: integral component of membrane