CKAP4

cytoskeleton associated protein 4

Basic information

Region (hg38): 12:106237881-106304279

Links

ENSG00000136026 ∙ NCBI:10970 ∙ OMIM:618595 ∙ HGNC:16991 ∙ Uniprot:Q07065 ∙ 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 CKAP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CKAP4 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	2	3
missense			41	4	1	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	5	3

Variants in CKAP4

This is a list of pathogenic ClinVar variants found in the CKAP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-106239095-A-C			Benign (Feb 13, 2018)
12-106239133-A-C		not specified	Uncertain significance (Aug 02, 2022)
12-106239134-T-G		not specified	Uncertain significance (Apr 18, 2023)
12-106239232-G-T		not specified	Uncertain significance (May 30, 2024)
12-106239254-G-T		not specified	Uncertain significance (Oct 05, 2023)
12-106239269-C-T		not specified	Uncertain significance (Jul 10, 2024)
12-106239298-G-A		not specified	Uncertain significance (Dec 20, 2023)
12-106239384-G-A			Likely benign (Dec 08, 2017)
12-106239400-G-A		not specified	Uncertain significance (Jun 05, 2023)
12-106239458-C-T		not specified	Uncertain significance (Jan 24, 2025)
12-106239473-G-A		not specified	Uncertain significance (Oct 13, 2023)
12-106239488-C-T		not specified	Uncertain significance (Jan 18, 2025)
12-106239493-C-T		not specified	Uncertain significance (Dec 02, 2022)
12-106239501-G-A			Benign (May 31, 2018)
12-106239515-T-C		not specified	Uncertain significance (Oct 11, 2024)
12-106239577-C-G		not specified	Uncertain significance (Jun 13, 2023)
12-106239587-C-T		not specified	Uncertain significance (Sep 14, 2022)
12-106239652-C-T		not specified	Likely benign (Jul 07, 2022)
12-106239673-G-C		not specified	Uncertain significance (Jul 05, 2024)
12-106239677-C-T		not specified	Likely benign (Dec 28, 2023)
12-106239689-A-C		not specified	Likely benign (Nov 10, 2024)
12-106239701-G-A		not specified	Uncertain significance (Dec 27, 2022)
12-106239724-A-C		not specified	Uncertain significance (May 23, 2023)
12-106239728-C-G		not specified	Uncertain significance (Nov 09, 2024)
12-106239739-C-T		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CKAP4	protein_coding	protein_coding	ENST00000378026	2	66403

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.509	0.491	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.852	249	290	0.859	0.0000182	3857
Missense in Polyphen		85	112.63	0.75471		1364
Synonymous	-0.417	142	136	1.05	0.00000913	1213
Loss of Function	2.85	3	14.9	0.202	6.46e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000550	0.0000544
Finnish	0.000140	0.000139
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.0000550	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: High-affinity epithelial cell surface receptor for APF.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Neutrophil degranulation;Post-translational protein phosphorylation;Post-translational protein modification;Surfactant metabolism;Metabolism of proteins;Innate Immune System;Immune System;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.282
• rvis_EVS: -0.91
• rvis_percentile_EVS: 10.03

Haploinsufficiency Scores

• pHI: 0.390
• hipred: Y
• hipred_score: 0.598
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.608

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ckap4
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); 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); growth/size/body region phenotype; hearing/vestibular/ear phenotype; embryo phenotype

Gene ontology

• Biological process: neutrophil degranulation;post-translational protein modification;cellular protein metabolic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum lumen;endoplasmic reticulum membrane;rough endoplasmic reticulum;lipid droplet;cytosol;cytoskeleton;plasma membrane;membrane;integral component of membrane;nuclear speck;azurophil granule membrane;specific granule membrane;cytoplasmic ribonucleoprotein granule;lamellar body;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: RNA binding