TMCO6

transmembrane and coiled-coil domains 6, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 5:140639434-140645408

Links

ENSG00000113119 ∙ NCBI:55374 ∙ ∙ HGNC:28814 ∙ Uniprot:Q96DC7 ∙ 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 TMCO6 gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMCO6 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			11	1		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	11	2	0

Variants in TMCO6

This is a list of pathogenic ClinVar variants found in the TMCO6 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140639534-A-G		not specified	Uncertain significance (Aug 05, 2023)
5-140639818-G-A			Likely benign (Jun 01, 2023)
5-140639819-G-A		not specified	Uncertain significance (Oct 05, 2021)
5-140639849-G-A		not specified	Uncertain significance (Apr 25, 2023)
5-140641680-C-T		not specified	Uncertain significance (Feb 10, 2023)
5-140641693-G-A		not specified	Uncertain significance (Dec 15, 2023)
5-140641716-G-C		not specified	Uncertain significance (Aug 02, 2021)
5-140641779-C-T		not specified	Uncertain significance (Nov 09, 2023)
5-140641877-G-A		not specified	Uncertain significance (Oct 28, 2023)
5-140641880-A-G		not specified	Uncertain significance (Jul 12, 2022)
5-140641943-C-T		not specified	Uncertain significance (Aug 12, 2021)
5-140641964-C-G		not specified	Uncertain significance (Aug 21, 2023)
5-140642348-G-A		not specified	Uncertain significance (Dec 05, 2022)
5-140642360-G-A		not specified	Uncertain significance (Feb 06, 2024)
5-140642374-G-C		not specified	Uncertain significance (Oct 17, 2023)
5-140642592-C-G		not specified	Uncertain significance (Aug 02, 2022)
5-140642627-G-C		not specified	Uncertain significance (Aug 12, 2021)
5-140642945-T-C		not specified	Uncertain significance (Feb 28, 2023)
5-140643595-G-C		not specified	Uncertain significance (Dec 31, 2023)
5-140643871-G-A		not specified	Uncertain significance (Jun 29, 2023)
5-140644180-G-A		not specified	Uncertain significance (Nov 06, 2023)
5-140644674-T-G		not specified	Likely benign (May 09, 2022)
5-140644687-G-A		not specified	Uncertain significance (Feb 06, 2024)
5-140645045-G-C		not specified	Uncertain significance (Jan 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMCO6	protein_coding	protein_coding	ENST00000394671	12	5982

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.27e-9	0.793	124719	0	95	124814	0.000381

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.430	249	269	0.926	0.0000143	3101
Missense in Polyphen		77	100.39	0.76704		1216
Synonymous	0.179	113	115	0.979	0.00000585	1074
Loss of Function	1.57	18	26.8	0.672	0.00000138	278

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000990	0.000989
Ashkenazi Jewish	0.00	0.00
East Asian	0.00111	0.00111
Finnish	0.00	0.00
European (Non-Finnish)	0.000302	0.000300
Middle Eastern	0.00111	0.00111
South Asian	0.000327	0.000327
Other	0.000661	0.000659

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.665
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.289
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.127

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmco6

Gene ontology

• Biological process: protein import into nucleus
• Cellular component: cell;integral component of membrane
• Molecular function: protein binding;nuclear import signal receptor activity