TMCC1

transmembrane and coiled-coil domain family 1, the group of Transmembrane and coiled-coil domain containing

Basic information

Region (hg38): 3:129647791-129893711

Links

ENSG00000172765 ∙ NCBI:23023 ∙ OMIM:616242 ∙ HGNC:29116 ∙ Uniprot:O94876 ∙ 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 TMCC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMCC1 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			16		1	17
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	17	0	1

Variants in TMCC1

This is a list of pathogenic ClinVar variants found in the TMCC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-129651503-C-G		not specified	Uncertain significance (Mar 16, 2022)
3-129651525-C-T		not specified	Uncertain significance (Dec 08, 2021)
3-129651793-C-G		not specified	Uncertain significance (Oct 26, 2021)
3-129670432-C-T		not specified	Uncertain significance (May 09, 2023)
3-129670439-C-T		not specified	Uncertain significance (Dec 09, 2023)
3-129670454-G-C		not specified	Uncertain significance (Mar 08, 2024)
3-129670465-A-G		not specified	Uncertain significance (Sep 27, 2021)
3-129670520-C-T		not specified	Uncertain significance (Dec 27, 2023)
3-129670895-G-A		not specified	Uncertain significance (Feb 27, 2023)
3-129671072-C-T		not specified	Uncertain significance (Jun 14, 2023)
3-129671077-C-T		not specified	Uncertain significance (Nov 22, 2022)
3-129671259-T-G		not specified	Uncertain significance (Feb 05, 2024)
3-129827886-T-C			Benign (Jun 26, 2020)
3-129827933-A-G		not specified	Uncertain significance (Oct 25, 2022)
3-129828042-G-A		not specified	Uncertain significance (Jun 13, 2022)
3-129828117-C-G		not specified	Uncertain significance (Jun 03, 2024)
3-129828193-C-A		not specified	Uncertain significance (Sep 01, 2021)
3-129828315-C-T		not specified	Uncertain significance (Oct 27, 2021)
3-129828372-G-T		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMCC1	protein_coding	protein_coding	ENST00000393238	4	245785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.845	0.155	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.06	199	363	0.548	0.0000204	4289
Missense in Polyphen		42	129.69	0.32385		1630
Synonymous	0.858	126	139	0.907	0.00000750	1308
Loss of Function	3.75	4	23.7	0.169	0.00000136	273

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000452	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.453
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• pHI: 0.275
• hipred: Y
• hipred_score: 0.685
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.375

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmcc1

Gene ontology

• Biological process: endoplasmic reticulum organization;protein homooligomerization;protein heterooligomerization
• Cellular component: endoplasmic reticulum membrane;rough endoplasmic reticulum;cytosol;integral component of membrane
• Molecular function: protein binding;protein homodimerization activity;protein heterodimerization activity