TMCO4

transmembrane and coiled-coil domains 4

Basic information

Region (hg38): 1:19682240-19799945

Links

ENSG00000162542NCBI:255104HGNC:27393Uniprot:Q5TGY1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMCO4 gene.

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
1
clinvar
1
missense
39
clinvar
2
clinvar
41
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 39 3 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)3178320
1-19683072-T-C not specified Likely benign (Jun 17, 2024)3326588
1-19683105-G-A not specified Uncertain significance (Jan 16, 2024)3178319
1-19683109-C-T not specified Uncertain significance (Jun 17, 2024)3326596
1-19683150-C-A not specified Uncertain significance (Jun 02, 2024)3326595
1-19683279-G-A not specified Uncertain significance (Jun 21, 2023)2598510
1-19683307-T-C Likely benign (Mar 01, 2024)3234404
1-19683315-G-A not specified Uncertain significance (May 31, 2022)2209035
1-19683320-T-A not specified Uncertain significance (Jul 26, 2022)2361898
1-19683356-C-T not specified Uncertain significance (Jan 29, 2024)2319179
1-19683363-C-T not specified Uncertain significance (Jun 07, 2024)3326590
1-19683364-G-T not specified Uncertain significance (Nov 15, 2023)3178318
1-19683383-C-T not specified Uncertain significance (Jul 27, 2021)2239653
1-19683393-C-T not specified Uncertain significance (Dec 16, 2022)3178317
1-19683404-A-T not specified Uncertain significance (Dec 17, 2023)2263865
1-19694492-C-T not specified Uncertain significance (Dec 09, 2023)3178316
1-19694504-A-T not specified Uncertain significance (Feb 27, 2023)2489174
1-19694523-G-A not specified Uncertain significance (Jan 31, 2023)2455223
1-19694537-A-G not specified Uncertain significance (Jun 03, 2024)3326591
1-19700814-G-C not specified Uncertain significance (Jan 24, 2024)3178315
1-19700841-C-T not specified Uncertain significance (Nov 18, 2022)2327600
1-19737424-G-C not specified Uncertain significance (Mar 20, 2023)2526995
1-19739831-C-T not specified Uncertain significance (Nov 29, 2023)3178314
1-19739900-T-C not specified Uncertain significance (Apr 24, 2024)3326594
1-19739960-C-A not specified Uncertain significance (Dec 14, 2022)2334907

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TMCO4protein_codingprotein_codingENST00000294543 13117733
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.67e-200.0029312518115661257480.00226
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1813773870.9740.00002324024
Missense in Polyphen149157.330.947081598
Synonymous0.1321691710.9870.00001141359
Loss of Function0.1743132.10.9670.00000189324

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.004020.00402
Ashkenazi Jewish0.002980.00298
East Asian0.001530.00152
Finnish0.001060.00106
European (Non-Finnish)0.003030.00300
Middle Eastern0.001530.00152
South Asian0.0007280.000719
Other0.002780.00277

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Tmco4
Phenotype

Gene ontology

Biological process
Cellular component
integral component of membrane
Molecular function