CAMSAP3

calmodulin regulated spectrin associated protein family member 3, the group of Protein phosphatase 1 regulatory subunits|MicroRNA protein coding host genes|CAMSAP family

Basic information

Region (hg38): 19:7595863-7618304

Previous symbols: [ "KIAA1543" ]

Links

ENSG00000076826 ∙ NCBI:57662 ∙ OMIM:612685 ∙ HGNC:29307 ∙ Uniprot:Q9P1Y5 ∙ 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 CAMSAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAMSAP3 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	4
missense			106	3	1	110
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	106	3	5

Variants in CAMSAP3

This is a list of pathogenic ClinVar variants found in the CAMSAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-7596010-A-C		not specified	Uncertain significance (Aug 28, 2021)
19-7605235-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-7605243-C-A		not specified	Uncertain significance (Mar 23, 2022)
19-7605262-C-T		not specified	Uncertain significance (Sep 14, 2024)
19-7605284-T-A		not specified	Uncertain significance (May 13, 2024)
19-7605451-C-A		not specified	Uncertain significance (Apr 25, 2023)
19-7606286-G-A		not specified	Uncertain significance (Nov 11, 2024)
19-7606303-G-A		not specified	Uncertain significance (Apr 14, 2022)
19-7606314-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-7606319-G-A		not specified	Uncertain significance (Oct 27, 2022)
19-7606513-C-G		not specified	Uncertain significance (May 14, 2024)
19-7606570-C-T		not specified	Uncertain significance (May 31, 2023)
19-7608154-C-A		not specified	Uncertain significance (Apr 06, 2024)
19-7608160-G-A		not specified	Uncertain significance (Oct 25, 2024)
19-7608178-C-T		not specified	Uncertain significance (Sep 24, 2024)
19-7608179-G-A			Benign (Jul 16, 2018)
19-7608221-C-T			Benign (Jul 07, 2018)
19-7608236-C-G		not specified	Uncertain significance (May 30, 2023)
19-7610554-G-A		not specified	Uncertain significance (Jul 20, 2021)
19-7610562-C-T		not specified	Uncertain significance (Nov 23, 2024)
19-7610563-G-A		not specified	Uncertain significance (Jul 26, 2024)
19-7610597-C-T			Benign (Jul 19, 2018)
19-7610598-G-A		not specified	Uncertain significance (Nov 19, 2022)
19-7610605-C-T		not specified	Uncertain significance (Oct 09, 2024)
19-7610784-G-A		not specified	Uncertain significance (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAMSAP3	protein_coding	protein_coding	ENST00000446248	19	22403

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000170	124768	0	7	124775	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.35	532	798	0.666	0.0000563	7970
Missense in Polyphen		227	381.28	0.59537		3993
Synonymous	1.03	335	360	0.931	0.0000266	2814
Loss of Function	6.18	3	50.3	0.0596	0.00000272	568

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000647	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.0000557	0.0000556
South Asian	0.0000327	0.0000327
Other	0.000171	0.000165

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:19041755, PubMed:23169647). Specifically recognizes growing microtubule minus-ends and autonomously decorates and stabilizes microtubule lattice formed by microtubule minus-end polymerization (PubMed:24486153). 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). In addition, it also reduces the velocity of microtubule polymerization (PubMed:24486153). Required for the biogenesis and the maintenance of zonula adherens by anchoring the minus-end of microtubules to zonula adherens and by recruiting the kinesin KIFC3 to those junctional sites (PubMed:19041755). Required for orienting the apical-to-basal polarity of microtubules in epithelial cells: acts by tethering non- centrosomal microtubules to the apical cortex, leading to their longitudinal orientation (PubMed:27802168, PubMed:26715742). Plays a key role in early embryos, which lack centrosomes: accumulates at the microtubule bridges that connect pairs of cells and enables the formation of a non-centrosomal microtubule-organizing center that directs intracellular transport in the early embryo (By similarity). Couples non-centrosomal microtubules with actin: interaction with MACF1 at the minus ends of non-centrosomal microtubules, tethers the microtubules to actin filaments, regulating focal adhesion size and cell migration (PubMed:27693509). Plays a key role in the generation of non- centrosomal microtubules by accumulating in the pericentrosomal region and cooperating with KATNA1 to release non-centrosomal microtubules from the centrosome (PubMed:28386021). Through the microtubule cytoskeleton, also regulates the organization of cellular organelles including the Golgi and the early endosomes (PubMed:28089391). Through interaction with AKAP9, involved in translocation of Golgi vesicles in epithelial cells, where microtubules are mainly non-centrosomal (PubMed:28089391). {ECO:0000250|UniProtKB:Q80VC9, ECO:0000269|PubMed:19041755, ECO:0000269|PubMed:23169647, ECO:0000269|PubMed:24486153, ECO:0000269|PubMed:26715742, ECO:0000269|PubMed:27693509, ECO:0000269|PubMed:27802168, ECO:0000269|PubMed:28089391, ECO:0000269|PubMed:28386021}.
• Pathway: Stabilization and expansion of the E-cadherin adherens junction (Consensus)

Recessive Scores

• pRec: 0.107

Haploinsufficiency Scores

• pHI: 0.154
• hipred: Y
• hipred_score: 0.717
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Camsap3
• Phenotype: growth/size/body region phenotype; liver/biliary system phenotype; skeleton phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; 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)

Gene ontology

• Biological process: microtubule cytoskeleton organization;negative regulation of microtubule depolymerization;embryo development ending in birth or egg hatching;negative regulation of phosphatase activity;regulation of cell migration;establishment or maintenance of microtubule cytoskeleton polarity;regulation of microtubule polymerization;cytoplasmic microtubule organization;neuron projection development;regulation of organelle organization;microtubule anchoring;establishment of epithelial cell apical/basal polarity;zonula adherens maintenance;regulation of focal adhesion assembly;regulation of microtubule cytoskeleton organization;epithelial cell-cell adhesion;protein transport along microtubule;regulation of Golgi organization
• Cellular component: cytoplasm;centrosome;zonula adherens;microtubule minus-end
• Molecular function: protein binding;calmodulin binding;spectrin binding;microtubule minus-end binding;actin filament binding