KRT39
protein-codingkeratin 39, the group of Keratins, type I
Gene summary
This gene encodes a member of the type I (acidic) keratin family, which belongs to the superfamily of intermediate filament (IF) proteins. Keratins are heteropolymeric structural proteins which form the intermediate filament. These filaments, along with actin microfilaments and microtubules, compose the cytoskeleton of epithelial cells. The type I keratin genes are clustered in a region of chromosome 17q12-q21. [provided by RefSeq, Jul 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.5 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 KRT39 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_213656.4. 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 | 67 | 5 | 72 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 67 | 5 | 0 | 72 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_998821.3 | 7 | MANE Select | |
| Ensembl | ENSP00000347823.2 | 7 | MANE Select | |
| Ensembl | ENSP00000464180.1 | 3 | Standard | |
| Ensembl | ENSP00000808372.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Estrogen signaling pathway - Homo sapiens (human)
- Keratinization
- Developmental Biology
Biological Process
- keratinization
- cornification
Molecular Function
- structural molecule activity
Cellular Component
- cytosol
- intermediate filament
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000355612
- Coding exons
- 7
- Length
- 8476
- Individuals with no LoFs
- 125608
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 140
- Defined
- 125748
- p
- 0.000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.160 | 263 | 270 | 0.973 | 0.0000155 | 3208 |
| Missense (PolyPhen) | 83 | 86.277 | 0.96202 | 1128 | ||
| Synonymous | 0.429 | 100 | 106 | 0.947 | 0.00000580 | 958 |
| Loss of Function | 0.703 | 21 | 24.8 | 0.848 | 0.00000131 | 268 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00029 | 0.00029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00049 | 0.00049 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00063 | 0.00062 | rare |
| South Asian | 0.0016 | 0.0015 | notable |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play a role in late hair differentiation.;
Recessive Scores
- pRec
- 0.0820
Intolerance Scores
- LoFtool
- 0.221
- RVIS EVS
- 0.78
- RVIS percentile EVS
- 87.21
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.213
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |