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): 8:135457456-135656722

Links

ENSG00000131773

∙ NCBI:10656 ∙ OMIM:610421 ∙ HGNC:18117 ∙ Uniprot:O75525 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KHDRBS3 gene.

not_specified (38 variants)

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. These statistics are base on transcript: NM_000006558.3. 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						0
missense			38 clinvar			38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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