TMCO3

transmembrane and coiled-coil domains 3

Basic information

Region (hg38): 13:113491021-113554590

Previous symbols: [ "C13orf11" ]

Links

ENSG00000150403 ∙ NCBI:55002 ∙ OMIM:617134 ∙ HGNC:20329 ∙ Uniprot:Q6UWJ1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Fuchs' endothelial dystrophy (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMCO3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMCO3 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			50	6		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	8	2

Variants in TMCO3

This is a list of pathogenic ClinVar variants found in the TMCO3 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-113491225-G-A			Uncertain significance (Oct 06, 2016)
13-113495588-G-A		not specified	Uncertain significance (Sep 11, 2024)
13-113495604-T-G		not specified	Uncertain significance (Aug 17, 2021)
13-113495640-T-G		not specified	Uncertain significance (May 24, 2023)
13-113495689-C-A		not specified	Uncertain significance (Apr 19, 2024)
13-113495690-C-T		not specified	Uncertain significance (Aug 05, 2024)
13-113495691-G-A		not specified	Uncertain significance (Oct 02, 2023)
13-113495697-G-A		not specified	Uncertain significance (Oct 01, 2024)
13-113495699-G-A		not specified	Uncertain significance (May 28, 2024)
13-113495711-A-G		not specified	Uncertain significance (Mar 06, 2023)
13-113495711-A-T		not specified	Uncertain significance (Oct 25, 2022)
13-113495720-C-T		not specified	Uncertain significance (Mar 07, 2024)
13-113495724-A-G			Likely benign (Feb 01, 2023)
13-113495730-T-C		not specified	Uncertain significance (Dec 19, 2022)
13-113495733-G-C		not specified	Uncertain significance (Aug 04, 2024)
13-113495805-T-C		not specified	Uncertain significance (Jul 22, 2024)
13-113495824-C-T			Likely benign (Feb 01, 2023)
13-113495826-T-C		not specified	Likely benign (Feb 21, 2024)
13-113495855-C-G		not specified	Uncertain significance (Jun 21, 2021)
13-113495862-A-G		not specified	Uncertain significance (Mar 20, 2024)
13-113495865-C-T		not specified	Uncertain significance (Aug 16, 2021)
13-113495957-A-C		not specified	Uncertain significance (Jan 18, 2022)
13-113495966-G-C		not specified	Uncertain significance (Jul 02, 2024)
13-113495982-G-A		not specified	Uncertain significance (Apr 27, 2024)
13-113495985-G-C		not specified	Uncertain significance (Jul 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMCO3	protein_coding	protein_coding	ENST00000434316	12	59233

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.94e-16	0.0469	125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.308	390	408	0.957	0.0000249	4368
Missense in Polyphen		93	114.18	0.81448		1310
Synonymous	0.720	163	175	0.931	0.0000121	1387
Loss of Function	0.699	26	30.1	0.863	0.00000158	351

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000440	0.000435
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000553	0.000544
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000355	0.000352
Middle Eastern	0.000553	0.000544
South Asian	0.000395	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable Na(+)/H(+) antiporter. {ECO:0000250}.

Recessive Scores

• pRec: 0.0917

Intolerance Scores

• loftool: 0.932
• rvis_EVS: -0.1
• rvis_percentile_EVS: 45.65

Haploinsufficiency Scores

• pHI: 0.0972
• hipred: N
• hipred_score: 0.251
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.638

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmco3

Gene ontology

• Biological process: proton transmembrane transport
• Cellular component: integral component of membrane
• Molecular function: solute:proton antiporter activity