CDAN1

codanin 1

Basic information

Region (hg38): 15:42723543-42737128

Links

ENSG00000140326 ∙ NCBI:146059 ∙ OMIM:607465 ∙ HGNC:1713 ∙ Uniprot:Q8IWY9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital dyserythropoietic anemia (Limited), mode of inheritance: AR
• anemia, congenital dyserythropoietic, type 1a (Definitive), mode of inheritance: AR
• congenital dyserythropoietic anemia type 1 (Supportive), mode of inheritance: AR
• anemia, congenital dyserythropoietic, type 1a (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Anemia, dyserythropoietic congenital, type Ia	AR	Hematologic	Individuals may require RBC transfusions in the neonatal period; Medical therapy (eg, with alpha-interferon) may be beneficial; Iron overload is common	Cardiovascular; Hematologic; Musculoskeletal; Renal	718245; 476312; 3096054; 2757972; 2124499; 7725852; 10971401; 10753260; 12434312; 16098079; 16141353; 18824595; 21378561; 21364188; 22504250

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDAN1 gene.

• not provided (13 variants)
• Anemia, congenital dyserythropoietic, type 1a (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDAN1 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			6	106	11	123
missense		7	227	11	5	250
nonsense	3		1			4
start loss						0
frameshift	12	5	2			19
inframe indel			3			3
splice donor/acceptor (+/-2bp)	1	3	1			5
splice region		1	13	17	2	33
non coding			28	56	31	115
Total	16	15	268	173	47

Highest pathogenic variant AF is 0.0000131

Variants in CDAN1

This is a list of pathogenic ClinVar variants found in the CDAN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-42723595-A-G		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 13, 2018)
15-42723664-T-C		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 13, 2018)
15-42723703-C-A		Congenital dyserythropoietic anemia, type I	Uncertain significance (Sep 01, 2022)
15-42723708-CTGTT-C		Congenital dyserythropoietic anemia	Uncertain significance (Jun 14, 2016)
15-42723738-G-A		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 13, 2018)
15-42723760-G-T		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 13, 2018)
15-42723769-C-T		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 13, 2018)
15-42723804-C-G		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 13, 2018)
15-42723811-G-C		Congenital dyserythropoietic anemia, type I	Uncertain significance (Apr 27, 2017)
15-42723834-T-C		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 13, 2018)
15-42723850-C-A		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 12, 2018)
15-42723891-T-C		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 13, 2018)
15-42723952-G-A		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 12, 2018)
15-42724025-TAAG-T		Congenital dyserythropoietic anemia	Likely benign (Jun 14, 2016)
15-42724142-T-C		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 13, 2018)
15-42724234-TAAAC-T		Congenital dyserythropoietic anemia	Uncertain significance (Jun 14, 2016)
15-42724268-C-G		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 13, 2018)
15-42724277-A-G		Congenital dyserythropoietic anemia, type I	Benign (May 10, 2021)
15-42724317-C-G		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 12, 2018)
15-42724349-T-C		Congenital dyserythropoietic anemia, type I	Benign (May 10, 2021)
15-42724397-A-G		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 12, 2018)
15-42724433-C-T		Congenital dyserythropoietic anemia, type I	Uncertain significance (Jan 12, 2018)
15-42724492-T-C			Uncertain significance (Aug 19, 2022)
15-42724500-G-GA			Uncertain significance (Jun 01, 2022)
15-42724509-A-G		Anemia, congenital dyserythropoietic, type 1a	Benign/Likely benign (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDAN1	protein_coding	protein_coding	ENST00000356231	28	13568

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.11e-12	1.00	125648	0	100	125748	0.000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.937	716	649	1.10	0.0000398	7775
Missense in Polyphen		384	375.43	1.0228		4588
Synonymous	-3.06	339	274	1.24	0.0000158	2645
Loss of Function	3.61	30	60.2	0.498	0.00000332	669

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000697	0.000692
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000275	0.000272
Finnish	0.000425	0.000416
European (Non-Finnish)	0.000458	0.000422
Middle Eastern	0.000275	0.000272
South Asian	0.000364	0.000359
Other	0.00130	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a negative regulator of ASF1 in chromatin assembly. {ECO:0000269|PubMed:22407294}.

Recessive Scores

• pRec: 0.184

Intolerance Scores

• loftool: 0.0662
• rvis_EVS: -0.83
• rvis_percentile_EVS: 11.54

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.379
• ghis: 0.645

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.362

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Cdan1
• 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

Gene ontology

• Biological process: chromatin organization;protein localization;negative regulation of DNA replication;chromatin assembly
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane;endomembrane system;integral component of membrane
• Molecular function: protein binding