TMCO2

transmembrane and coiled-coil domains 2

Basic information

Region (hg38): 1:40245947-40251684

Links

ENSG00000188800 ∙ NCBI:127391 ∙ ∙ HGNC:23312 ∙ Uniprot:Q7Z6W1 ∙ 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 TMCO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMCO2 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						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in TMCO2

This is a list of pathogenic ClinVar variants found in the TMCO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-40248096-G-A		not specified	Uncertain significance (Jun 13, 2024)
1-40251316-C-A		not specified	Uncertain significance (Jul 14, 2021)
1-40251328-G-T		not specified	Uncertain significance (May 09, 2024)
1-40251416-G-A		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMCO2	protein_coding	protein_coding	ENST00000372766	2	5745

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000547	0.464	125626	0	108	125734	0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.410	78	88.9	0.878	0.00000409	1173
Missense in Polyphen		22	23.036	0.95501		282
Synonymous	0.307	32	34.3	0.933	0.00000161	359
Loss of Function	0.398	7	8.23	0.850	5.32e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000249	0.000246
Ashkenazi Jewish	0.00707	0.00707
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.0000544	0.0000544
South Asian	0.000134	0.000131
Other	0.000981	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.539
• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.95

Haploinsufficiency Scores

• pHI: 0.334
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmco2

Gene ontology

• Cellular component: nucleus;integral component of membrane