TMEM200C

transmembrane protein 200C

Basic information

Region (hg38): 18:5882071-5895955

Links

ENSG00000206432NCBI:645369HGNC:37208Uniprot:A6NKL6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMEM200C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM200C 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
clinvar
2
missense
2
clinvar
2
nonsense
0
start loss
0
frameshift
0
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 0 5 0

Variants in TMEM200C

This is a list of pathogenic ClinVar variants found in the TMEM200C region.

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

Position Type Phenotype Significance ClinVar
18-5890865-C-A Likely benign (Dec 01, 2022)2648535
18-5890866-T-G Likely benign (Dec 01, 2022)2648536
18-5891101-G-C Likely benign (Dec 01, 2022)2648537
18-5891373-AGGCGGCGGCGGCCGC-A Likely benign (May 01, 2023)2648538
18-5891623-C-T EBV-positive nodal T- and NK-cell lymphoma Likely benign (-)2681612
18-5891629-G-A Likely benign (May 01, 2023)2648539

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TMEM200Cprotein_codingprotein_codingENST00000581347 113884
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.1060.785124485021244870.00000803
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1012632581.020.00001553872
Missense in Polyphen8297.970.836991055
Synonymous-1.621451221.190.000008231432
Loss of Function1.2525.020.3983.13e-792

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002900.0000290
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

pHI
hipred
hipred_score
ghis
0.495

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
gene_indispensability_pred
N
gene_indispensability_score
0.114

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Tmem200c
Phenotype

Gene ontology

Biological process
Cellular component
integral component of membrane
Molecular function