TMEM143
protein-codingtransmembrane protein 143
Gene summary
Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~31.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TMEM143 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018273.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 93 | 3 | 96 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 97 | 3 | 0 | 100 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060743.2 | 8 | MANE Select | |
| Ensembl | ENSP00000293261.2 | 8 | MANE Select | |
| RefSeq | NP_001290467.1 | 7 | Standard | |
| RefSeq | NP_001290468.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- biological_process
Molecular Function
- molecular_function
Cellular Component
- mitochondrion
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000293261
- Coding exons
- 8
- Length
- 31882
- Individuals with no LoFs
- 125168
- Homozygous LoFs
- 9
- Heterozygous LoFs
- 570
- Defined
- 125747
- p
- 0.00230
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.205 | 268 | 278 | 0.965 | 0.0000160 | 2885 |
| Missense (PolyPhen) | 83 | 95.931 | 0.86521 | 987 | ||
| Synonymous | -0.384 | 137 | 131 | 1.04 | 0.00000787 | 1020 |
| Loss of Function | 0.154 | 18 | 18.7 | 0.962 | 8.88e-7 | 202 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.0012 | 0.0012 | notable |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.020 | 0.020 | notable |
| Finnish | 0.0016 | 0.0015 | notable |
| European (Non-Finnish) | 0.00080 | 0.00077 | rare |
| South Asian | 0.0011 | 0.0010 | notable |
| Other | 0.0035 | 0.0033 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0745
Intolerance Scores
- LoFtool
- 0.766
- RVIS EVS
- -0.42
- RVIS percentile EVS
- 25.64
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.513
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |