NCKAP5

NCK associated protein 5

Basic information

Region (hg38): 2:132671787-133568463

Links

ENSG00000176771 ∙ NCBI:344148 ∙ OMIM:608789 ∙ HGNC:29847 ∙ Uniprot:O14513 ∙ 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 NCKAP5 gene.

• Inborn genetic diseases (84 variants)
• not provided (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCKAP5 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				4	7	11
missense			80	10	7	97
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	80	15	14

Variants in NCKAP5

This is a list of pathogenic ClinVar variants found in the NCKAP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-132725636-C-T		not specified	Uncertain significance (Dec 07, 2021)
2-132725656-A-G		not specified	Uncertain significance (Jul 14, 2021)
2-132728824-C-T		not specified	Uncertain significance (Dec 01, 2022)
2-132728835-A-T			Benign (Jul 13, 2018)
2-132728859-G-A		not specified	Uncertain significance (Dec 22, 2023)
2-132728904-G-A		not specified	Uncertain significance (Jan 22, 2024)
2-132728905-T-C		not specified	Uncertain significance (May 03, 2023)
2-132731761-G-A			Benign (Aug 09, 2018)
2-132731821-T-C		not specified	Uncertain significance (Sep 14, 2022)
2-132731824-C-T		not specified	Likely benign (Dec 08, 2023)
2-132731845-C-T		not specified	Likely benign (Jan 09, 2024)
2-132731971-G-A		not specified	Uncertain significance (Apr 25, 2022)
2-132731991-G-A		not specified	Uncertain significance (Dec 21, 2022)
2-132773817-T-C		not specified	Uncertain significance (Aug 12, 2021)
2-132773818-A-G		not specified	Uncertain significance (Dec 18, 2023)
2-132773827-C-T		not specified	Uncertain significance (Feb 22, 2023)
2-132773891-T-G		not specified	Uncertain significance (May 25, 2022)
2-132781059-T-A		not specified	Uncertain significance (Jun 29, 2023)
2-132781095-T-A			Likely benign (Dec 31, 2019)
2-132781130-G-A			Benign (Dec 31, 2019)
2-132781955-G-A		not specified	Uncertain significance (Mar 01, 2024)
2-132781973-G-A			Benign (Dec 31, 2019)
2-132781980-A-G		not specified	Uncertain significance (Jan 04, 2022)
2-132781991-C-A		not specified	Uncertain significance (Mar 28, 2023)
2-132781994-T-C		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCKAP5	protein_coding	protein_coding	ENST00000409261	18	896661

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000847	1.00	124598	0	42	124640	0.000169

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.368	1038	1.01e+3	1.03	0.0000534	12400
Missense in Polyphen		285	296.67	0.96067		3958
Synonymous	-0.192	403	398	1.01	0.0000233	3803
Loss of Function	5.33	23	71.7	0.321	0.00000408	917

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000347	0.000346
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.000197	0.000195
Middle Eastern	0.000223	0.000223
South Asian	0.000278	0.000261
Other	0.000183	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.994
• rvis_EVS: 0.65
• rvis_percentile_EVS: 84.13

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.273
• ghis: 0.418

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nckap5

Gene ontology

• Biological process: microtubule bundle formation;microtubule depolymerization;biological_process
• Cellular component: cellular_component;microtubule plus-end