CIAO3

cytosolic iron-sulfur assembly component 3, the group of Cytosolic iron-sulfur assembly components

Basic information

Region (hg38): 16:729759-741329

Previous symbols: [ "NARFL" ]

Links

ENSG00000103245 ∙ NCBI:64428 ∙ OMIM:611118 ∙ HGNC:14179 ∙ Uniprot:Q9H6Q4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• pulmonary arteriovenous malformation (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CIAO3 gene.

• Inborn genetic diseases (14 variants)
• not provided (7 variants)
• High myopia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CIAO3 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			13	4	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	13	5	3

Variants in CIAO3

This is a list of pathogenic ClinVar variants found in the CIAO3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-730425-G-A		not specified	Uncertain significance (Jul 09, 2021)
16-730439-G-C		not specified	Likely benign (Feb 05, 2024)
16-730446-C-T		not specified	Uncertain significance (Apr 03, 2023)
16-730469-G-A		not specified	Uncertain significance (Jan 26, 2023)
16-730493-T-C		not specified	Uncertain significance (Jan 23, 2023)
16-730510-C-T			Benign (Dec 31, 2019)
16-730545-C-T			Likely benign (Nov 09, 2018)
16-730575-C-T			Likely benign (Dec 04, 2018)
16-730664-G-A			Benign (Dec 04, 2018)
16-730885-G-A		not specified	Uncertain significance (Aug 02, 2021)
16-730890-C-T		not specified	Uncertain significance (Aug 07, 2023)
16-730923-C-T		High myopia • not specified	Uncertain significance (Feb 16, 2023)
16-731620-C-T		not specified	Uncertain significance (Dec 06, 2022)
16-731626-G-A		not specified	Uncertain significance (Oct 31, 2023)
16-731652-G-A		not specified	Uncertain significance (Jul 19, 2022)
16-731665-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-731695-C-T		not specified	Likely benign (Aug 04, 2023)
16-733310-C-T		not specified	Uncertain significance (Jan 31, 2024)
16-733342-T-C		not specified	Likely benign (Jan 03, 2022)
16-733400-C-T		not specified	Uncertain significance (Dec 19, 2022)
16-734220-C-T			Likely benign (May 14, 2018)
16-734255-C-G		not specified	Uncertain significance (Jan 18, 2023)
16-734284-C-T		not specified	Uncertain significance (Oct 03, 2023)
16-734800-G-A		not specified	Uncertain significance (Jan 18, 2023)
16-734811-C-T		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CIAO3	protein_coding	protein_coding	ENST00000251588	11	11577

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.89e-9	0.646	125665	0	49	125714	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.226	286	297	0.963	0.0000190	3062
Missense in Polyphen		92	112.91	0.81481		1217
Synonymous	-1.85	159	132	1.20	0.00000970	943
Loss of Function	1.32	17	24.0	0.709	0.00000137	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000233	0.000229
Middle Eastern	0.000435	0.000435
South Asian	0.000229	0.000229
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the cytosolic iron-sulfur protein assembly (CIA) complex, a multiprotein complex that mediates the incorporation of iron-sulfur cluster into extramitochondrial Fe/S proteins. Seems to negatively regulate the level of HIF1A expression, although this effect could be indirect. {ECO:0000269|PubMed:16956324, ECO:0000269|PubMed:18270200}.

Recessive Scores

• pRec: 0.184

Intolerance Scores

• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.61

Haploinsufficiency Scores

• pHI: 0.0601
• hipred: N
• hipred_score: 0.237
• ghis: 0.508

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Narfl
• 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); normal phenotype

Zebrafish Information Network

• Gene name: narfl
• Affected structure: subintestinal vein
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: response to hypoxia;hematopoietic progenitor cell differentiation;regulation of gene expression;iron-sulfur cluster assembly;oxygen homeostasis
• Cellular component: CIA complex
• Molecular function: protein binding;metal ion binding;4 iron, 4 sulfur cluster binding