KHDRBS3
KH RNA binding domain containing, signal transduction associated 3, the group of Signal transduction and activation of RNA metabolism family
Basic information
Region (hg38): 8:135457455-135656722
Links
Phenotypes
GenCC
Source:
No genCC data.
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 KHDRBS3 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 | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 0 | 0 |
Variants in KHDRBS3
This is a list of pathogenic ClinVar variants found in the KHDRBS3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-135457882-C-G | not specified | Uncertain significance (Jun 29, 2022) | ||
| 8-135457919-C-T | not specified | Uncertain significance (Jul 19, 2023) | ||
| 8-135457930-C-T | not specified | Uncertain significance (Jun 03, 2022) | ||
| 8-135542703-G-A | not specified | Uncertain significance (Jan 06, 2023) | ||
| 8-135542765-G-A | not specified | Uncertain significance (Jul 17, 2023) | ||
| 8-135557523-G-A | not specified | Uncertain significance (Sep 17, 2021) | ||
| 8-135581888-G-A | not specified | Uncertain significance (Oct 05, 2023) | ||
| 8-135582000-G-A | not specified | Uncertain significance (Dec 02, 2021) | ||
| 8-135582048-C-T | not specified | Uncertain significance (Mar 16, 2024) | ||
| 8-135582058-G-T | not specified | Uncertain significance (Mar 25, 2024) | ||
| 8-135606998-A-G | not specified | Uncertain significance (Jul 05, 2022) | ||
| 8-135607019-A-G | not specified | Uncertain significance (Jan 19, 2024) | ||
| 8-135645063-G-A | not specified | Uncertain significance (Dec 13, 2023) | ||
| 8-135645070-A-G | not specified | Uncertain significance (Apr 12, 2024) | ||
| 8-135645081-G-A | not specified | Uncertain significance (Jun 13, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KHDRBS3 | protein_coding | protein_coding | ENST00000355849 | 9 | 199266 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.442 | 0.557 | 125737 | 0 | 11 | 125748 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.32 | 136 | 187 | 0.728 | 0.00000981 | 2218 |
| Missense in Polyphen | 45 | 76.676 | 0.58688 | 930 | ||
| Synonymous | 0.0917 | 68 | 69.0 | 0.986 | 0.00000366 | 677 |
| Loss of Function | 3.13 | 4 | 18.6 | 0.215 | 9.31e-7 | 243 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000963 | 0.0000615 |
| Ashkenazi Jewish | 0.000398 | 0.000397 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000328 | 0.0000327 |
| Other | 0.000206 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. Binds preferentially to the 5'-[AU]UAAA-3' motif in vitro. Binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. Binds poly(A). RNA-binding abilities are down-regulated by tyrosine kinase PTK6 (PubMed:10564820, PubMed:19561594, PubMed:26758068). Involved in splice site selection of vascular endothelial growth factor (PubMed:15901763). In vitro regulates CD44 alternative splicing by direct binding to purine-rich exonic enhancer (By similarity). Can regulate alternative splicing of neurexins NRXN1- 3 in the laminin G-like domain 6 containing the evolutionary conserved neurexin alternative spliced segment 4 (AS4) involved in neurexin selective targeting to postsynaptic partners such as neuroligins and LRRTM family members (PubMed:26758068). Targeted, cell-type specific splicing regulation of NRXN1 at AS4 is involved in neuronal glutamatergic synapse function and plasticity (By similarity). May regulate expression of KHDRBS2/SLIM-1 in defined brain neuron populations by modifying its alternative splicing (By similarity). Can bind FABP9 mRNA (By similarity). May play a role as a negative regulator of cell growth. Inhibits cell proliferation. {ECO:0000250|UniProtKB:Q9JLP1, ECO:0000250|UniProtKB:Q9R226, ECO:0000269|PubMed:10564820, ECO:0000269|PubMed:15901763, ECO:0000269|PubMed:19561594, ECO:0000269|PubMed:26758068}.;
- Pathway
- Signaling by PTK6;Signal Transduction;PTK6 Regulates Proteins Involved in RNA Processing;Signaling by Non-Receptor Tyrosine Kinases
(Consensus)
Recessive Scores
- pRec
- 0.166
Intolerance Scores
- loftool
- 0.441
- rvis_EVS
- -0.6
- rvis_percentile_EVS
- 17.75
Haploinsufficiency Scores
- pHI
- 0.225
- hipred
- Y
- hipred_score
- 0.875
- ghis
- 0.595
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.943
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Khdrbs3
- Phenotype
- reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- mRNA processing;regulation of mRNA splicing, via spliceosome;protein complex oligomerization
- Cellular component
- nucleus;nucleoplasm
- Molecular function
- RNA binding;protein binding;SH3 domain binding;protein domain specific binding;identical protein binding