TXNDC16
protein-codingthioredoxin domain containing 16, the group of Thioredoxin domain containing
Gene summary
Located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Jul 2025]
- KIAA1344
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~123.1 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 TXNDC16 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020784.3. 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 | 1 | 5 | 6 | |||
| missense | 117 | 4 | 121 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 0 | 0 | 125 | 9 | 0 | 134 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065835.2 | 19 | MANE Select | |
| Ensembl | ENSP00000281741.4 | 19 | MANE Select | |
| RefSeq | NP_001153519.1 | 19 | Standard | |
| Ensembl | ENSP00000451619.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- biological_process
- cell redox homeostasis
Molecular Function
- protein binding
Cellular Component
- endoplasmic reticulum lumen
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000281741
- Coding exons
- 19
- Length
- 121933
- Individuals with no LoFs
- 125687
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 54
- Defined
- 125741
- p
- 0.000215
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.243 | 416 | 402 | 1.03 | 0.0000185 | 5391 |
| Missense (PolyPhen) | 87 | 81.357 | 1.0694 | 1091 | ||
| Synonymous | -1.10 | 161 | 144 | 1.12 | 0.00000692 | 1540 |
| Loss of Function | 3.34 | 15 | 36.9 | 0.407 | 0.00000156 | 534 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00028 | 0.00027 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00022 | 0.00022 | rare |
| South Asian | 0.00047 | 0.00046 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0903
Intolerance Scores
- LoFtool
- 0.835
- RVIS EVS
- 0.83
- RVIS percentile EVS
- 88.11
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.238
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |