KHNYN

KH and NYN domain containing

Basic information

Region (hg38): 14:24429286-24441843

Previous symbols: [ "KIAA0323" ]

Links

ENSG00000100441 ∙ NCBI:23351 ∙ OMIM:619579 ∙ HGNC:20166 ∙ Uniprot:O15037 ∙ 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 KHNYN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KHNYN 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				1		1
missense			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			18			18
Total	0	0	52	1	0

Variants in KHNYN

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

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

Position	Type	Phenotype	Significance	ClinVar
14-24430767-C-G		not specified	Uncertain significance (Nov 09, 2023)
14-24430818-C-A		not specified	Uncertain significance (Aug 05, 2024)
14-24430824-G-A		not specified	Uncertain significance (Aug 02, 2023)
14-24430827-C-T		not specified	Uncertain significance (Jul 12, 2023)
14-24430830-A-C		not specified	Uncertain significance (May 23, 2024)
14-24430840-T-C		not specified	Uncertain significance (Jun 18, 2024)
14-24430878-C-G		not specified	Uncertain significance (Jun 13, 2022)
14-24430920-A-T		not specified	Uncertain significance (Apr 22, 2022)
14-24431521-A-G		not specified	Uncertain significance (Nov 09, 2022)
14-24431598-C-T		not specified	Uncertain significance (Jun 22, 2023)
14-24431641-C-A		not specified	Uncertain significance (Aug 02, 2021)
14-24431649-A-G		not specified	Uncertain significance (Mar 01, 2023)
14-24431661-C-T		not specified	Uncertain significance (Jun 09, 2022)
14-24431664-G-A		not specified	Uncertain significance (Feb 10, 2023)
14-24431701-C-T		not specified	Uncertain significance (Aug 14, 2024)
14-24431731-G-T		not specified	Uncertain significance (Oct 03, 2024)
14-24431860-G-T		not specified	Uncertain significance (Dec 16, 2021)
14-24431878-T-G		not specified	Uncertain significance (Oct 05, 2021)
14-24431899-G-C		not specified	Uncertain significance (Apr 24, 2024)
14-24431904-G-A		not specified	Uncertain significance (Mar 25, 2024)
14-24431914-G-A		not specified	Uncertain significance (May 20, 2024)
14-24431926-A-C		not specified	Uncertain significance (Oct 21, 2024)
14-24431958-G-A		not specified	Uncertain significance (May 31, 2023)
14-24432021-G-A		not specified	Uncertain significance (Aug 02, 2021)
14-24432051-G-A		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KHNYN	protein_coding	protein_coding	ENST00000251343	7	12049

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.61e-8	0.957	125534	3	211	125748	0.000851

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.347	385	405	0.951	0.0000231	4360
Missense in Polyphen		125	181.16	0.69		1854
Synonymous	0.388	154	160	0.961	0.00000850	1436
Loss of Function	2.02	17	28.6	0.594	0.00000155	291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000643	0.000642
Ashkenazi Jewish	0.0130	0.0126
East Asian	0.000111	0.000109
Finnish	0.000417	0.000416
European (Non-Finnish)	0.000426	0.000413
Middle Eastern	0.000111	0.000109
South Asian	0.0000981	0.0000980
Other	0.000989	0.000978

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0949

Intolerance Scores

• loftool: 0.798
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.88

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.208
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.776

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Khnyn

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function;RNA binding