NCKAP5L

NCK associated protein 5 like

Basic information

Region (hg38): 12:49791145-49828750

Previous symbols: [ "KIAA1602" ]

Links

ENSG00000167566 ∙ NCBI:57701 ∙ OMIM:615104 ∙ HGNC:29321 ∙ Uniprot:Q9HCH0 ∙ 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 NCKAP5L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCKAP5L 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					2	2
missense			92	5	1	98
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	92	5	3

Variants in NCKAP5L

This is a list of pathogenic ClinVar variants found in the NCKAP5L region.

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

Position	Type	Phenotype	Significance	ClinVar
12-49791912-G-A		not specified	Uncertain significance (May 23, 2023)
12-49791943-C-T		not specified	Uncertain significance (May 16, 2022)
12-49792003-G-A		not specified	Uncertain significance (Jun 03, 2022)
12-49792466-C-T		not specified	Uncertain significance (Dec 15, 2023)
12-49792481-G-T		not specified	Uncertain significance (Jul 13, 2021)
12-49792516-G-T		not specified	Uncertain significance (Dec 01, 2022)
12-49792731-G-A		not specified	Uncertain significance (Jun 13, 2023)
12-49792735-A-G		not specified	Uncertain significance (Apr 19, 2024)
12-49792795-G-A		not specified	Uncertain significance (Nov 18, 2022)
12-49792815-C-T		not specified	Uncertain significance (May 17, 2023)
12-49792840-G-A		not specified	Uncertain significance (Nov 30, 2022)
12-49792863-G-A		not specified	Uncertain significance (Mar 07, 2024)
12-49792863-G-C		not specified	Uncertain significance (Nov 22, 2023)
12-49792875-C-T		not specified	Uncertain significance (Sep 20, 2023)
12-49792878-G-A		not specified	Uncertain significance (Apr 08, 2024)
12-49792885-T-G		not specified	Uncertain significance (Jan 30, 2024)
12-49793400-G-C		not specified	Uncertain significance (Nov 12, 2021)
12-49793411-C-T		not specified	Likely benign (Aug 13, 2021)
12-49793421-G-A		not specified	Uncertain significance (Mar 01, 2024)
12-49793751-C-T		not specified	Uncertain significance (Oct 25, 2023)
12-49793828-G-A		not specified	Uncertain significance (Dec 03, 2021)
12-49793850-G-A		not specified	Uncertain significance (Jul 11, 2023)
12-49794822-C-G		not specified	Uncertain significance (Sep 28, 2022)
12-49794825-T-G		not specified	Uncertain significance (Jun 10, 2024)
12-49794829-C-T		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCKAP5L	protein_coding	protein_coding	ENST00000335999	11	37605

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.632	0.368	124797	0	30	124827	0.000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.741	656	712	0.922	0.0000424	8212
Missense in Polyphen		227	264.24	0.85905		3192
Synonymous	0.167	307	311	0.988	0.0000187	3001
Loss of Function	4.78	9	42.7	0.211	0.00000248	485

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000164	0.000161
Ashkenazi Jewish	0.000102	0.0000993
East Asian	0.000339	0.000222
Finnish	0.0000474	0.0000464
European (Non-Finnish)	0.000157	0.000150
Middle Eastern	0.000339	0.000222
South Asian	0.000109	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates microtubule organization and stabilization. Promotes microtubule growth and bundling formation and stabilizes microtubules by increasing intense acetylation of microtubules (PubMed:26482847, PubMed:26485573). Both tubulin-binding and homodimer formation are required for NCKAP5L-mediated microtubule bundle formation (PubMed:26485573). {ECO:0000269|PubMed:26482847, ECO:0000269|PubMed:26485573}.

Intolerance Scores

• loftool: 0.609
• rvis_EVS: -0.79
• rvis_percentile_EVS: 12.62

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.372
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nckap5l

Gene ontology

• Biological process: microtubule bundle formation;microtubule depolymerization
• Cellular component: cytoplasm;centrosome;microtubule plus-end
• Molecular function: protein binding