CIBAR1

CBY1 interacting BAR domain containing 1

Basic information

Region (hg38): 8:93698561-93731527

Previous symbols: [ "FAM92A1", "FAM92A" ]

Links

ENSG00000188343 ∙ NCBI:137392 ∙ OMIM:617273 ∙ HGNC:30452 ∙ Uniprot:A1XBS5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• postaxial polydactyly type A (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Polydactyly, postaxial, type A9	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	Musculoskeletal	30395363

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CIBAR1 gene.

• Polydactyly, postaxial, type A9 (2 variants)
• Postaxial polydactyly type A (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CIBAR1 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		1
missense			17	1	1	19
nonsense	2					2
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	2	1	17	2	1

Highest pathogenic variant AF is 0.0000131

Variants in CIBAR1

This is a list of pathogenic ClinVar variants found in the CIBAR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-93701253-C-G		not specified	Uncertain significance (Jul 15, 2021)
8-93701307-A-G		not specified	Uncertain significance (Jul 25, 2023)
8-93701312-C-T		not specified	Uncertain significance (Dec 28, 2022)
8-93701333-G-A		not specified	Uncertain significance (Jan 09, 2024)
8-93701383-G-A		CIBAR1-related disorder	Likely benign (May 10, 2022)
8-93701433-A-G		not specified	Uncertain significance (Aug 01, 2022)
8-93701454-C-G		not specified	Uncertain significance (May 25, 2022)
8-93703647-G-A		not specified	Uncertain significance (Oct 12, 2022)
8-93704930-A-C		not specified	Uncertain significance (Feb 22, 2023)
8-93704942-C-T		Polydactyly, postaxial, type A9	Pathogenic (May 22, 2022)
8-93704943-G-A		not specified	Uncertain significance (Apr 25, 2023)
8-93704949-C-A		not specified	Uncertain significance (Sep 27, 2021)
8-93704964-A-G		not specified	Uncertain significance (Mar 28, 2023)
8-93704967-TAGAA-T		Polydactyly, postaxial, type A9	Likely pathogenic (Mar 23, 2022)
8-93704985-G-A		not specified	Uncertain significance (Jun 17, 2024)
8-93705000-G-A		not specified	Uncertain significance (Mar 20, 2024)
8-93709810-C-T		Polydactyly, postaxial, type A9 • Postaxial polydactyly type A	Pathogenic (Apr 20, 2023)
8-93726401-G-A		CIBAR1-related disorder	Benign (Oct 28, 2019)
8-93726418-C-A		not specified	Uncertain significance (Dec 09, 2023)
8-93726419-C-T		not specified	Uncertain significance (Dec 18, 2023)
8-93726434-G-A		not specified	Uncertain significance (Oct 06, 2022)
8-93726443-T-G		CIBAR1-related disorder	Likely benign (Dec 24, 2019)
8-93728215-G-T		not specified	Uncertain significance (Mar 31, 2023)
8-93728227-A-G		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CIBAR1	protein_coding	protein_coding	ENST00000518322	9	32967

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.79e-8	0.665	124600	0	38	124638	0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.967	113	146	0.775	0.00000767	1858
Missense in Polyphen		27	39.889	0.67689		565
Synonymous	0.484	48	52.5	0.915	0.00000276	532
Loss of Function	1.21	14	19.8	0.707	0.00000133	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000128	0.000128
Ashkenazi Jewish	0.00	0.00
East Asian	0.000173	0.000167
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000170	0.000168
Middle Eastern	0.000173	0.000167
South Asian	0.000411	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in ciliogenesis (PubMed:27528616). In cooperation with CBY1 may facilitate ciliogenesis likely by the recruitment and fusion of endosomal vesicles at distal appendages during early stages of ciliogenesis (PubMed:27528616). {ECO:0000269|PubMed:27528616}.

Recessive Scores

• pRec: 0.0900

Intolerance Scores

• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.11

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.350
• ghis: 0.472

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Fam92a
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: cilium assembly
• Cellular component: nucleus;cytoplasm;centriole;ciliary basal body;ciliary base
• Molecular function: protein binding