CPLANE2

ciliogenesis and planar polarity effector complex subunit 2, the group of Ciliogenesis and planar polarity effector complex subunits

Basic information

Region (hg38): 1:16231692-16237183

Previous symbols: [ "C1orf89", "RSG1" ]

Links

ENSG00000132881 ∙ NCBI:79363 ∙ ∙ HGNC:28127 ∙ Uniprot:Q9BU20 ∙ 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 CPLANE2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPLANE2 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						0
missense			35	1		36
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	35	1	0

Variants in CPLANE2

This is a list of pathogenic ClinVar variants found in the CPLANE2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-16232099-G-C		not specified	Uncertain significance (Feb 27, 2024)
1-16232130-T-C		not specified	Uncertain significance (Aug 11, 2024)
1-16232146-C-T		not specified	Likely benign (Apr 25, 2023)
1-16232157-C-T		not specified	Uncertain significance (Apr 27, 2023)
1-16232164-G-A		not specified	Uncertain significance (Mar 28, 2024)
1-16232178-C-T		not specified	Uncertain significance (Sep 10, 2024)
1-16232179-G-A		not specified	Uncertain significance (Apr 08, 2022)
1-16232179-G-T		not specified	Uncertain significance (Mar 16, 2022)
1-16232193-C-T		not specified	Uncertain significance (May 25, 2022)
1-16232217-C-T		not specified	Uncertain significance (May 26, 2023)
1-16232218-G-A		not specified	Uncertain significance (Mar 18, 2024)
1-16232236-A-G		not specified	Uncertain significance (Jun 29, 2022)
1-16232262-C-T		not specified	Uncertain significance (Nov 06, 2023)
1-16232272-C-T		not specified	Uncertain significance (Jul 20, 2021)
1-16232277-G-A		not specified	Uncertain significance (Dec 06, 2022)
1-16232523-C-A		not specified	Uncertain significance (Feb 01, 2025)
1-16232526-T-A		not specified	Uncertain significance (Jan 08, 2024)
1-16232558-C-T		not specified	Uncertain significance (Jun 11, 2024)
1-16232559-G-A		not specified	Uncertain significance (Dec 09, 2023)
1-16232595-G-A		not specified	Uncertain significance (Jun 02, 2023)
1-16232633-T-C		not specified	Uncertain significance (Aug 19, 2023)
1-16232907-C-A		not specified	Uncertain significance (Dec 14, 2023)
1-16232907-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-16232952-G-A		not specified	Uncertain significance (Jan 23, 2025)
1-16232966-C-T		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPLANE2	protein_coding	protein_coding	ENST00000375599	5	5463

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000886	0.334	125722	0	23	125745	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.617	152	175	0.869	0.0000112	1650
Missense in Polyphen		47	49.786	0.94404		492
Synonymous	1.61	53	70.1	0.756	0.00000432	555
Loss of Function	0.205	8	8.65	0.925	3.68e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000289	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000277	0.000277
European (Non-Finnish)	0.0000805	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential effector of the planar cell polarity signaling pathway. Plays a role in targeted membrane trafficking most probably at the level of vesicle fusion with membranes. Involved in cilium biogenesis by regulating the transport of cargo proteins to the basal body and to the apical tips of cilia. More generally involved in exocytosis in secretory cells (By similarity). {ECO:0000250|UniProtKB:Q6GNL4}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.0856
• hipred: N
• hipred_score: 0.167
• ghis: 0.563

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Rsg1
• Phenotype: craniofacial phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; respiratory system phenotype; immune system phenotype; skeleton phenotype; limbs/digits/tail phenotype; digestive/alimentary phenotype; vision/eye phenotype; hematopoietic system 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)

Gene ontology

• Biological process: exocytosis;protein transport;regulation of exocytosis;regulation of vesicle fusion;cellular protein localization;cilium assembly
• Cellular component: nucleoplasm;cytoplasm;ciliary basal body
• Molecular function: GTPase activity;protein binding;GTP binding