TMCO4

transmembrane and coiled-coil domains 4

Basic information

Region (hg38): 1:19682239-19799945

Links

ENSG00000162542 ∙ NCBI:255104 ∙ ∙ HGNC:27393 ∙ Uniprot:Q5TGY1 ∙ 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 TMCO4 gene.

• Inborn genetic diseases (28 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMCO4 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			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	0

Variants in TMCO4

This is a list of pathogenic ClinVar variants found in the TMCO4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-19683066-G-C		not specified	Uncertain significance (Feb 12, 2024)
1-19683105-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-19683279-G-A		not specified	Uncertain significance (Jun 21, 2023)
1-19683307-T-C			Likely benign (Mar 01, 2024)
1-19683315-G-A		not specified	Uncertain significance (May 31, 2022)
1-19683320-T-A		not specified	Uncertain significance (Jul 26, 2022)
1-19683356-C-T		not specified	Uncertain significance (Jan 29, 2024)
1-19683364-G-T		not specified	Uncertain significance (Nov 15, 2023)
1-19683383-C-T		not specified	Uncertain significance (Jul 27, 2021)
1-19683393-C-T		not specified	Uncertain significance (Dec 16, 2022)
1-19683404-A-T		not specified	Uncertain significance (Dec 17, 2023)
1-19694492-C-T		not specified	Uncertain significance (Dec 09, 2023)
1-19694504-A-T		not specified	Uncertain significance (Feb 27, 2023)
1-19694523-G-A		not specified	Uncertain significance (Jan 31, 2023)
1-19700814-G-C		not specified	Uncertain significance (Jan 24, 2024)
1-19700841-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-19737424-G-C		not specified	Uncertain significance (Mar 20, 2023)
1-19739831-C-T		not specified	Uncertain significance (Nov 29, 2023)
1-19739960-C-A		not specified	Uncertain significance (Dec 14, 2022)
1-19740902-C-T		not specified	Uncertain significance (Jun 03, 2022)
1-19745565-C-T		not specified	Uncertain significance (Oct 03, 2023)
1-19746495-T-C		not specified	Uncertain significance (Jul 26, 2022)
1-19746498-T-C		not specified	Likely benign (May 08, 2023)
1-19746504-T-C		not specified	Uncertain significance (Jul 14, 2021)
1-19746507-C-T		not specified	Uncertain significance (May 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMCO4	protein_coding	protein_coding	ENST00000294543	13	117733

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.67e-20	0.00293	125181	1	566	125748	0.00226

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.181	377	387	0.974	0.0000232	4024
Missense in Polyphen		149	157.33	0.94708		1598
Synonymous	0.132	169	171	0.987	0.0000114	1359
Loss of Function	0.174	31	32.1	0.967	0.00000189	324

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00402	0.00402
Ashkenazi Jewish	0.00298	0.00298
East Asian	0.00153	0.00152
Finnish	0.00106	0.00106
European (Non-Finnish)	0.00303	0.00300
Middle Eastern	0.00153	0.00152
South Asian	0.000728	0.000719
Other	0.00278	0.00277

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.934
• rvis_EVS: 0.45
• rvis_percentile_EVS: 78.05

Haploinsufficiency Scores

• pHI: 0.193
• hipred: N
• hipred_score: 0.251
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.273

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmco4

Gene ontology

• Cellular component: integral component of membrane