KRTAP23-1
Basic information
Region (hg38): 21:30348399-30348606
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRTAP23-1 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 | 0 | |||||
missense | 6 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 3 | 3 | 0 |
Variants in KRTAP23-1
This is a list of pathogenic ClinVar variants found in the KRTAP23-1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
21-30348431-C-T | not specified | Uncertain significance (Jan 07, 2022) | ||
21-30348438-G-T | not specified | Uncertain significance (Jul 12, 2023) | ||
21-30348531-G-A | not specified | Likely benign (May 31, 2023) | ||
21-30348569-T-C | not specified | Likely benign (Jul 09, 2021) | ||
21-30348587-C-G | not specified | Likely benign (Jul 09, 2021) | ||
21-30348591-A-G | not specified | Uncertain significance (Sep 22, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
KRTAP23-1 | protein_coding | protein_coding | ENST00000334160 | 1 | 208 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.0723 | 32 | 30.9 | 1.04 | 0.00000156 | 401 |
Missense in Polyphen | ||||||
Synonymous | -0.121 | 16 | 15.4 | 1.04 | 7.81e-7 | 142 |
Loss of Function |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | ||
East Asian | ||
Finnish | ||
European (Non-Finnish) | ||
Middle Eastern | ||
South Asian | ||
Other |
dbNSFP
Source:
- Function
- FUNCTION: In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated proteins (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high- sulfur and high-glycine-tyrosine keratins.;
Intolerance Scores
- loftool
- 0.324
- rvis_EVS
- 0.5
- rvis_percentile_EVS
- 79.79
Haploinsufficiency Scores
- pHI
- 0.170
- hipred
- N
- hipred_score
- 0.123
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.00000886
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Low | Low |
Primary Immunodeficiency | Medium | Low | Medium |
Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- keratinization
- Cellular component
- cytosol;intermediate filament
- Molecular function
- protein binding