CDIN1

CDAN1 interacting nuclease 1

Basic information

Region (hg38): 15:36579626-36810248

Previous symbols: [ "C15orf41" ]

Links

ENSG00000186073 ∙ NCBI:84529 ∙ OMIM:615626 ∙ HGNC:26929 ∙ Uniprot:Q9Y2V0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital dyserythropoietic anemia type Ib	AR	Hematologic	Individuals have been described as manifesting with early childhood onset, severe anemia requiring treatment via RBC transfusion	Hematologic; Musculoskeletal	9220189; 16643456; 16754775; 23716552

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDIN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDIN1 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	8
missense		2	24	1	1	28
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	3	1	5
non coding		1	1	17	28	47
Total	0	3	27	22	33

Variants in CDIN1

This is a list of pathogenic ClinVar variants found in the CDIN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-36579756-C-T		Congenital dyserythropoietic anemia type type 1B	Benign (Jul 14, 2021)
15-36579886-A-G			Conflicting classifications of pathogenicity (Aug 01, 2023)
15-36579905-A-C		CDIN1-related disorder	Likely benign (Jan 29, 2024)
15-36579906-G-A			Uncertain significance (Jan 27, 2021)
15-36579919-C-G		Congenital dyserythropoietic anemia type type 1B	Uncertain significance (Jul 11, 2019)
15-36579958-C-T		Congenital dyserythropoietic anemia type type 1B	Uncertain significance (Jan 09, 2024)
15-36579978-C-T			Likely benign (Jun 10, 2023)
15-36580168-T-C			Benign (Jun 18, 2021)
15-36644260-T-G			Likely benign (Mar 11, 2022)
15-36644288-G-C			Likely benign (Apr 10, 2022)
15-36644317-G-A			Likely benign (Nov 28, 2023)
15-36644340-T-A			Likely benign (Nov 20, 2022)
15-36644592-C-T			Benign (Jun 18, 2021)
15-36645204-G-T		not specified • Congenital dyserythropoietic anemia type type 1B	Benign (Jan 31, 2024)
15-36645207-G-T			Likely benign (Oct 13, 2023)
15-36645207-G-GT			Benign (Jan 04, 2024)
15-36645225-A-G			Uncertain significance (Mar 18, 2022)
15-36645230-T-G			Uncertain significance (Feb 09, 2023)
15-36645251-A-G			Uncertain significance (Mar 04, 2022)
15-36645255-T-C			Likely benign (Nov 20, 2023)
15-36645260-C-T		CDIN1-related disorder	Likely benign (Jan 29, 2024)
15-36645261-G-A			Benign (Dec 06, 2023)
15-36645281-A-G		Congenital dyserythropoietic anemia type type 1B	Uncertain significance (Mar 26, 2024)
15-36645405-A-C			Benign (Jun 18, 2021)
15-36645494-TTG-T			Benign (Jun 19, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDIN1	protein_coding	protein_coding	ENST00000566621	11	230638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.29e-7	0.791	124627	0	27	124654	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.473	129	145	0.890	0.00000722	1825
Missense in Polyphen		41	48.36	0.84781		603
Synonymous	1.15	46	57.0	0.807	0.00000319	510
Loss of Function	1.38	13	19.6	0.664	9.22e-7	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000586	0.0000586
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000947	0.0000928
European (Non-Finnish)	0.000184	0.000177
Middle Eastern	0.00	0.00
South Asian	0.000105	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Anemia, congenital dyserythropoietic, 1B (CDAN1B) [MIM:615631]: An autosomal recessive blood disorder characterized by morphological abnormalities of erythroblasts, ineffective erythropoiesis, macrocytic anemia and secondary hemochromatosis. It is occasionally associated with bone abnormalities, especially of the hands and feet (acrodysostosis), nail hypoplasia, and scoliosis. Ultrastructural features include internuclear chromatin bridges connecting some nearly completely separated erythroblasts and an abnormal appearance (spongy or Swiss-cheese appearance) of the heterochromatin in a high proportion of the erythroblasts. {ECO:0000269|PubMed:23716552}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.614
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.205
• hipred: N
• hipred_score: 0.237
• ghis: 0.486

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: BC052040