KHSRP

KH-type splicing regulatory protein, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 19:6413102-6424811

Links

ENSG00000088247 ∙ NCBI:8570 ∙ OMIM:603445 ∙ HGNC:6316 ∙ Uniprot:Q92945 ∙ 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 KHSRP gene.

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.

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				3	4	7
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	3	4

Variants in KHSRP

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

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

Position	Type	Phenotype	Significance	ClinVar
19-6415160-G-A		not specified	Uncertain significance (Nov 17, 2022)
19-6415209-C-T		not specified	Uncertain significance (Oct 12, 2022)
19-6415231-C-T			Likely benign (Mar 01, 2023)
19-6415295-A-G		not specified	Uncertain significance (Dec 01, 2022)
19-6415432-T-C			Benign (Apr 20, 2021)
19-6415652-G-A		not specified	Likely benign (Dec 08, 2023)
19-6415858-C-G		not specified	Uncertain significance (Dec 19, 2022)
19-6415866-T-G			Benign (May 15, 2018)
19-6416541-A-G			Benign (Jun 13, 2018)
19-6416873-G-A		not specified	Uncertain significance (May 13, 2024)
19-6417030-T-C		not specified	Uncertain significance (Feb 16, 2023)
19-6417984-G-A			Likely benign (Apr 01, 2023)
19-6418509-T-C		not specified	Uncertain significance (Sep 07, 2022)
19-6419244-G-A			Benign (Sep 04, 2018)
19-6420106-G-C		not specified	Uncertain significance (May 14, 2024)
19-6421285-G-T		not specified	Uncertain significance (Feb 12, 2024)
19-6421294-T-C		not specified	Uncertain significance (Dec 21, 2023)
19-6422390-C-T		not specified	Uncertain significance (Apr 13, 2023)
19-6424544-C-A		not specified	Uncertain significance (Feb 26, 2024)
19-6424617-C-A		not specified	Uncertain significance (Aug 22, 2023)
19-6424635-C-A		not specified	Uncertain significance (Apr 07, 2023)
19-6424644-C-T		not specified	Uncertain significance (Oct 02, 2023)
19-6424671-G-T		not specified	Uncertain significance (Jun 03, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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