TMCC2

transmembrane and coiled-coil domain family 2, the group of Transmembrane and coiled-coil domain containing

Basic information

Region (hg38): 1:205227945-205285632

Links

ENSG00000133069 ∙ NCBI:9911 ∙ OMIM:619429 ∙ HGNC:24239 ∙ Uniprot:O75069 ∙ 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 TMCC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMCC2 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
missense			36	1	1	38
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	37	1	4

Variants in TMCC2

This is a list of pathogenic ClinVar variants found in the TMCC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-205228578-G-A		not specified	Likely benign (Apr 16, 2024)
1-205228629-A-G		not specified	Uncertain significance (Jan 03, 2024)
1-205228634-G-A		not specified	Uncertain significance (Mar 29, 2023)
1-205228668-C-A		not specified	Uncertain significance (Apr 12, 2022)
1-205228679-A-G		not specified	Likely benign (May 04, 2022)
1-205228712-G-A		not specified	Uncertain significance (Nov 17, 2023)
1-205241518-T-C		not specified	Uncertain significance (Jan 19, 2024)
1-205241526-G-A		not specified	Uncertain significance (May 27, 2022)
1-205241575-G-A		not specified	Uncertain significance (Jul 19, 2023)
1-205241581-G-A		not specified	Uncertain significance (Jun 28, 2022)
1-205241638-T-C		not specified	Uncertain significance (Oct 26, 2022)
1-205241671-G-A		not specified	Uncertain significance (May 23, 2024)
1-205241699-C-A			Uncertain significance (Oct 13, 2016)
1-205241778-A-G		not specified	Uncertain significance (Dec 22, 2023)
1-205241785-G-A		not specified	Uncertain significance (May 08, 2023)
1-205241788-G-A		not specified	Uncertain significance (Sep 17, 2021)
1-205241790-G-A		not specified	Uncertain significance (Mar 18, 2024)
1-205241802-A-G		not specified	Uncertain significance (May 21, 2024)
1-205241815-G-T		not specified	Uncertain significance (Aug 15, 2023)
1-205241817-G-A		not specified	Uncertain significance (Oct 04, 2022)
1-205241824-G-A		not specified	Uncertain significance (Aug 08, 2022)
1-205241841-C-T		not specified	Uncertain significance (Mar 18, 2024)
1-205241872-G-A		not specified	Uncertain significance (Jan 19, 2022)
1-205241893-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-205241901-C-T		not specified	Uncertain significance (May 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMCC2	protein_coding	protein_coding	ENST00000358024	5	45168

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.295	0.705	125730	0	13	125743	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	338	475	0.712	0.0000332	4589
Missense in Polyphen		89	158.27	0.56235		1490
Synonymous	-0.196	219	215	1.02	0.0000155	1512
Loss of Function	3.27	5	21.3	0.235	9.19e-7	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000375	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the regulation of the proteolytic processing of the amyloid precursor protein (APP) possibly also implicating APOE. {ECO:0000269|PubMed:21593558}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.216
• rvis_EVS: -1.06
• rvis_percentile_EVS: 7.48

Haploinsufficiency Scores

• pHI: 0.245
• hipred: Y
• hipred_score: 0.707
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.619

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmcc2

Gene ontology

• Biological process: amyloid precursor protein metabolic process
• Cellular component: endoplasmic reticulum;integral component of membrane
• Molecular function: protein binding