KHSRP
Basic information
Region (hg38): 19:6413102-6424811
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (43 variants)
- not_provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KHSRP gene is commonly pathogenic or not. These statistics are base on transcript: NM_001366299.1. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | |||||
| missense | 42 | 42 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 43 | 3 | 3 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KHSRP | protein_coding | protein_coding | ENST00000398148 | 20 | 11447 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.00000112 | 124606 | 0 | 1 | 124607 | 0.00000401 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.83 | 173 | 384 | 0.450 | 0.0000237 | 4524 |
| Missense in Polyphen | 45 | 155.16 | 0.29003 | 1703 | ||
| Synonymous | -1.95 | 193 | 161 | 1.20 | 0.0000122 | 1454 |
| Loss of Function | 5.73 | 0 | 38.2 | 0.00 | 0.00000186 | 446 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000165 | 0.000165 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to the dendritic targeting element and may play a role in mRNA trafficking (By similarity). Part of a ternary complex that binds to the downstream control sequence (DCS) of the pre-mRNA. Mediates exon inclusion in transcripts that are subject to tissue-specific alternative splicing. May interact with single- stranded DNA from the far-upstream element (FUSE). May activate gene expression. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'- UTR, possibly by recruiting degradation machinery to ARE- containing mRNAs. {ECO:0000250, ECO:0000269|PubMed:11003644, ECO:0000269|PubMed:8940189, ECO:0000269|PubMed:9136930}.;
- Pathway
- Preimplantation Embryo;KSRP (KHSRP) binds and destabilizes mRNA;Metabolism of RNA;Regulation of mRNA stability by proteins that bind AU-rich elements
(Consensus)
Recessive Scores
- pRec
- 0.155
Intolerance Scores
- loftool
- 0.190
- rvis_EVS
- -0.69
- rvis_percentile_EVS
- 15.12
Haploinsufficiency Scores
- pHI
- 0.452
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.672
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.995
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Khsrp
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype;
Gene ontology
- Biological process
- RNA splicing, via transesterification reactions;regulation of transcription, DNA-templated;mRNA processing;mRNA catabolic process;RNA splicing;miRNA metabolic process;negative regulation of low-density lipoprotein particle clearance;regulation of mRNA stability;negative regulation of nitric oxide biosynthetic process;mRNA transport;positive regulation of mRNA catabolic process;3'-UTR-mediated mRNA destabilization;cellular response to cytokine stimulus;regulation of miRNA metabolic process
- Cellular component
- exosome (RNase complex);nucleoplasm;cytosol;cytoplasmic stress granule;membrane
- Molecular function
- DNA binding;RNA binding;protein binding;mRNA 3'-UTR AU-rich region binding