CAMSAP1

calmodulin regulated spectrin associated protein 1, the group of CAMSAP family

Basic information

Region (hg38): 9:135808486-135907546

Links

ENSG00000130559 ∙ NCBI:157922 ∙ OMIM:613774 ∙ HGNC:19946 ∙ Uniprot:Q5T5Y3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cortical dysplasia, complex, with other brain malformations 12 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cortical dysplasia, complex, with other brain malformations 12	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; Neurologic	36283405

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CAMSAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAMSAP1 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	3	4
missense			77	7	2	86
nonsense		3				3
start loss						0
frameshift		2				2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			2			2
Total	0	5	79	8	5

Variants in CAMSAP1

This is a list of pathogenic ClinVar variants found in the CAMSAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-135811343-G-A		Inborn genetic diseases	Uncertain significance (Sep 14, 2023)
9-135811346-C-T		Inborn genetic diseases	Uncertain significance (Feb 21, 2024)
9-135811523-T-C		Inborn genetic diseases	Uncertain significance (Jun 22, 2024)
9-135811608-G-T		Inborn genetic diseases	Uncertain significance (Dec 02, 2021)
9-135815191-C-G		Inborn genetic diseases	Uncertain significance (Mar 21, 2024)
9-135815899-C-T		Inborn genetic diseases	Uncertain significance (Sep 07, 2022)
9-135815922-G-C		Inborn genetic diseases	Uncertain significance (Apr 15, 2024)
9-135815942-G-C		Inborn genetic diseases	Uncertain significance (Mar 07, 2024)
9-135817986-G-T		Inborn genetic diseases	Uncertain significance (May 13, 2024)
9-135817987-G-T		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
9-135818047-T-A		Inborn genetic diseases	Uncertain significance (Feb 09, 2024)
9-135818051-G-A			Benign (Dec 31, 2019)
9-135818055-G-C		CAMSAP1-related neuronal migration disorder	Likely pathogenic (Sep 15, 2022)
9-135818443-G-A		Inborn genetic diseases	Uncertain significance (Feb 27, 2023)
9-135818504-G-C		Inborn genetic diseases	Uncertain significance (Apr 15, 2024)
9-135818594-C-A		Inborn genetic diseases	Uncertain significance (Sep 06, 2022)
9-135820928-C-T		Inborn genetic diseases	Uncertain significance (Nov 07, 2022)
9-135820941-G-C		Inborn genetic diseases	Uncertain significance (Jan 24, 2024)
9-135820994-C-T		Inborn genetic diseases	Uncertain significance (Sep 17, 2021)
9-135821000-C-T		Inborn genetic diseases	Likely benign (Aug 02, 2022)
9-135821047-A-G		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
9-135821074-C-A			Uncertain significance (Jul 27, 2022)
9-135821169-A-C		Inborn genetic diseases	Uncertain significance (Feb 01, 2023)
9-135821171-A-G		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)
9-135821188-C-A		Inborn genetic diseases	Uncertain significance (Mar 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAMSAP1	protein_coding	protein_coding	ENST00000389532	17	98742

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000149	125577	0	16	125593	0.0000637

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.15	763	950	0.803	0.0000609	10474
Missense in Polyphen		141	246.69	0.57156		2616
Synonymous	-0.674	425	408	1.04	0.0000298	3147
Loss of Function	6.25	8	60.4	0.132	0.00000335	739

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000145	0.000139
European (Non-Finnish)	0.0000630	0.0000617
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Key microtubule-organizing protein that specifically binds the minus-end of non-centrosomal microtubules and regulates their dynamics and organization (PubMed:19508979, PubMed:21834987, PubMed:24486153, PubMed:24706919, PubMed:24117850). Specifically recognizes growing microtubule minus-ends and stabilizes microtubules (PubMed:24486153, PubMed:24706919). Acts on free microtubule minus-ends that are not capped by microtubule- nucleating proteins or other factors and protects microtubule minus-ends from depolymerization (PubMed:24486153, PubMed:24706919). In contrast to CAMSAP2 and CAMSAP3, tracks along the growing tips of minus-end microtubules without significantly affecting the polymerization rate: binds at the very tip of the microtubules minus-end and acts as a minus-end tracking protein (- TIP) that dissociates from microtubules after allowing tubulin incorporation (PubMed:24486153, PubMed:24706919). Through interaction with spectrin may regulate neurite outgrowth (PubMed:24117850). {ECO:0000269|PubMed:19508979, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:24117850, ECO:0000269|PubMed:24486153, ECO:0000269|PubMed:24706919}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: -2.65
• rvis_percentile_EVS: 0.77

Haploinsufficiency Scores

• pHI: 0.193
• hipred: Y
• hipred_score: 0.554
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.382

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Camsap1

Gene ontology

• Biological process: microtubule cytoskeleton organization;cytoskeleton organization;negative regulation of microtubule depolymerization;regulation of cell morphogenesis;regulation of microtubule polymerization;cytoplasmic microtubule organization;neuron projection development
• Cellular component: cytoplasm;microtubule;microtubule minus-end
• Molecular function: calmodulin binding;microtubule binding;spectrin binding;microtubule minus-end binding