KHDRBS2

KH RNA binding domain containing, signal transduction associated 2, the group of Signal transduction and activation of RNA metabolism family

Basic information

Region (hg38): 6:61679960-62286225

Links

ENSG00000112232 ∙ NCBI:202559 ∙ OMIM:610487 ∙ HGNC:18114 ∙ Uniprot:Q5VWX1 ∙ 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 KHDRBS2 gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KHDRBS2 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in KHDRBS2

This is a list of pathogenic ClinVar variants found in the KHDRBS2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-61681007-A-G		not specified	Uncertain significance (Oct 05, 2023)
6-61697206-T-G		not specified	Uncertain significance (May 09, 2022)
6-61697209-G-A		not specified	Uncertain significance (May 28, 2023)
6-61732698-C-T		not specified	Uncertain significance (Jul 07, 2022)
6-61732704-T-A		not specified	Uncertain significance (Aug 04, 2023)
6-61732732-A-T		not specified	Uncertain significance (Sep 16, 2021)
6-61894654-T-C		not specified	Uncertain significance (Feb 27, 2024)
6-61894673-C-T		not specified	Uncertain significance (Apr 25, 2022)
6-61894708-C-T		not specified	Uncertain significance (Dec 15, 2022)
6-61894720-A-G		not specified	Uncertain significance (Oct 27, 2022)
6-61894756-C-T		not specified	Uncertain significance (Nov 14, 2023)
6-61894775-G-A		not specified	Uncertain significance (Apr 18, 2023)
6-61894780-G-A		not specified	Uncertain significance (Nov 27, 2023)
6-61894801-G-C		not specified	Uncertain significance (Sep 17, 2021)
6-61894802-G-T		not specified	Uncertain significance (Sep 22, 2022)
6-61894817-T-C		not specified	Uncertain significance (Jun 18, 2021)
6-61894826-C-T		not specified	Uncertain significance (Jun 21, 2023)
6-61894828-C-T		not specified	Uncertain significance (Feb 21, 2024)
6-61901251-G-A		not specified	Uncertain significance (Nov 09, 2023)
6-61901276-T-A		not specified	Uncertain significance (Nov 27, 2023)
6-61901298-C-T		not specified	Uncertain significance (Dec 18, 2023)
6-61978074-G-T		not specified	Uncertain significance (Jun 18, 2021)
6-61978159-C-G		not specified	Uncertain significance (Oct 25, 2022)
6-61978176-C-T		not specified	Uncertain significance (Apr 25, 2023)
6-61978178-T-C		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KHDRBS2	protein_coding	protein_coding	ENST00000281156	9	606268

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0385	0.960	125701	1	46	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0168	196	197	0.997	0.0000106	2221
Missense in Polyphen		61	72.602	0.8402		848
Synonymous	-2.37	93	68.1	1.37	0.00000347	684
Loss of Function	2.82	6	19.4	0.309	9.76e-7	251

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000317	0.0000317
Ashkenazi Jewish	0.00299	0.00288
East Asian	0.0000551	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.0000551	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000494	0.000489

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 both poly(A) and poly(U) homopolymers. Phosphorylation by PTK6 inhibits its RNA-binding ability (By similarity). Induces an increased concentration-dependent incorporation of exon in CD44 pre-mRNA by direct binding to purine-rich exonic enhancer. Can regulate alternative splicing of NRXN1 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. Regulates cell-type specific alternative splicing of NRXN1 at AS4 and acts synergystically with SAM68 in exon skipping. In contrast acts antagonistically with SAM68 in NRXN3 exon skipping at AS4. Its phosphorylation by FYN inhibits its ability to regulate splice site selection. May function as an adapter protein for Src kinases during mitosis. {ECO:0000250|UniProtKB:Q920F3, ECO:0000250|UniProtKB:Q9WU01}.
• Pathway: Signaling by PTK6;Signal Transduction;PTK6 Regulates Proteins Involved in RNA Processing;Signaling by Non-Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.500
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.92

Haploinsufficiency Scores

• pHI: 0.846
• hipred: Y
• hipred_score: 0.648
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.977

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Khdrbs2
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype

Gene ontology

• Biological process: mRNA processing;regulation of mRNA splicing, via spliceosome
• Cellular component: nucleoplasm
• Molecular function: protein binding;poly(A) binding;poly(U) RNA binding;SH3 domain binding;SH2 domain binding;identical protein binding;protein heterodimerization activity