KNCN

kinocilin

Basic information

Region (hg38): 1:46545641-46551647

Links

ENSG00000162456 ∙ NCBI:148930 ∙ OMIM:611455 ∙ HGNC:26488 ∙ Uniprot:A6PVL3 ∙ 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 KNCN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KNCN 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			11	1		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	11	1	0

Variants in KNCN

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

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

Position	Type	Phenotype	Significance	ClinVar
1-46547743-G-T		not specified	Uncertain significance (Dec 11, 2023)
1-46547744-C-T		not specified	Likely benign (Aug 28, 2023)
1-46547749-C-T		not specified	Uncertain significance (Feb 23, 2023)
1-46547758-G-A		not specified	Uncertain significance (Aug 04, 2023)
1-46547786-C-T		not specified	Uncertain significance (Apr 08, 2024)
1-46547803-C-T		not specified	Uncertain significance (Jun 29, 2022)
1-46549207-T-C		not specified	Uncertain significance (Mar 24, 2023)
1-46549224-T-G		not specified	Uncertain significance (May 09, 2022)
1-46551138-G-C		not specified	Uncertain significance (Feb 15, 2023)
1-46551142-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-46551161-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-46551170-C-G		not specified	Uncertain significance (Oct 14, 2021)
1-46551182-C-T		not specified	Uncertain significance (May 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KNCN	protein_coding	protein_coding	ENST00000396314	3	5884

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000479	0.140	124477	0	94	124571	0.000377

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.372	66	58.0	1.14	0.00000361	632
Missense in Polyphen		19	18.209	1.0435		161
Synonymous	0.132	25	25.9	0.967	0.00000187	218
Loss of Function	-1.69	5	2.26	2.22	9.57e-8	30

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.000101	0.0000995
East Asian	0.000114	0.000111
Finnish	0.0000933	0.0000928
European (Non-Finnish)	0.000315	0.000310
Middle Eastern	0.000114	0.000111
South Asian	0.00161	0.00154
Other	0.000169	0.000166

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in stabilizing dense microtubular networks or in vesicular trafficking. {ECO:0000250}.

Intolerance Scores

• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.11

Haploinsufficiency Scores

• pHI: 0.0906
• hipred: Y
• hipred_score: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kncn

Gene ontology

• Cellular component: cytoplasm;integral component of membrane;apical plasma membrane;cuticular plate;ciliary basal body;neuronal cell body;apical part of cell;kinocilium