CKAP2L

cytoskeleton associated protein 2 like

Basic information

Region (hg38): 2:112736348-112764664

Links

ENSG00000169607 ∙ NCBI:150468 ∙ OMIM:616174 ∙ HGNC:26877 ∙ Uniprot:Q8IYA6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Filippi syndrome (Definitive), mode of inheritance: AR
• Filippi syndrome (Moderate), mode of inheritance: AD
• Filippi syndrome (Strong), mode of inheritance: AR
• Filippi syndrome (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Filippi syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dental; Dermatologic; Musculoskeletal; Neurologic	15365457; 18553552; 25439729

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CKAP2L gene.

• Filippi syndrome (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CKAP2L 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				25	4	29
missense		1	84	6	11	102
nonsense						0
start loss						0
frameshift	2	4	1			7
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1					1
splice region			1	4		5
non coding				6	16	22
Total	3	5	86	37	31

Highest pathogenic variant AF is 0.00000657

Variants in CKAP2L

This is a list of pathogenic ClinVar variants found in the CKAP2L region.

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

Position	Type	Phenotype	Significance	ClinVar
2-112738554-A-T			Benign (Nov 10, 2018)
2-112738863-G-A			Uncertain significance (Jul 09, 2022)
2-112738875-C-T			Benign (Jan 22, 2024)
2-112738876-G-A		not specified	Benign (Jan 29, 2024)
2-112738888-A-T			Uncertain significance (Jul 12, 2022)
2-112738942-G-T		Inborn genetic diseases	Uncertain significance (Jan 03, 2022)
2-112738943-T-A			Benign (Jul 25, 2022)
2-112738945-C-G		Inborn genetic diseases	Uncertain significance (Feb 06, 2024)
2-112738950-A-G			Uncertain significance (Sep 01, 2022)
2-112738970-C-T			Likely benign (Mar 01, 2024)
2-112738977-C-T			Benign (Jun 01, 2024)
2-112738989-G-A		Inborn genetic diseases	Uncertain significance (Oct 21, 2021)
2-112738991-C-T			Likely benign (Sep 29, 2023)
2-112738995-C-T		Filippi syndrome	Uncertain significance (Sep 01, 2021)
2-112738998-C-T		Inborn genetic diseases	Uncertain significance (Mar 01, 2023)
2-112739003-A-G			Benign (Jan 15, 2024)
2-112739008-T-C		Inborn genetic diseases	Uncertain significance (Mar 20, 2023)
2-112739034-G-A			Uncertain significance (Dec 10, 2023)
2-112739055-G-T		CKAP2L-related disorder	Benign/Likely benign (Dec 07, 2023)
2-112739377-T-A			Benign (Jun 20, 2021)
2-112740760-C-T			Benign (Nov 10, 2018)
2-112740806-G-A			Likely benign (Oct 17, 2023)
2-112740822-G-A		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
2-112740854-T-A		Inborn genetic diseases	Uncertain significance (Aug 02, 2021)
2-112740866-T-G		Inborn genetic diseases	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CKAP2L	protein_coding	protein_coding	ENST00000302450	9	28325

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000159	1.00	125714	0	33	125747	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0890	394	389	1.01	0.0000194	4873
Missense in Polyphen		92	88.152	1.0436		1127
Synonymous	1.15	127	145	0.879	0.00000754	1430
Loss of Function	3.17	12	31.1	0.386	0.00000154	407

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000202	0.000202
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000176
Middle Eastern	0.00	0.00
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule-associated protein required for mitotic spindle formation and cell-cycle progression in neural progenitor cells. {ECO:0000269|PubMed:25439729}.
• Disease: DISEASE: Filippi syndrome (FLPIS) [MIM:272440]: A rare disorder characterized by microcephaly, pre- and postnatal growth failure, syndactyly, and distinctive facial features, including a broad nasal bridge and underdeveloped alae nasi. Some affected individuals have intellectual disability, seizures, undescended testicles in males, and teeth and hair abnormalities. {ECO:0000269|PubMed:25439729}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0749

Intolerance Scores

• loftool: 0.762
• rvis_EVS: 1.38
• rvis_percentile_EVS: 94.62

Haploinsufficiency Scores

• pHI: 0.0446
• hipred: N
• hipred_score: 0.233
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.107

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ckap2l

Gene ontology

• Cellular component: spindle pole;centrosome;cytosol;mitotic spindle