ODC1

ornithine decarboxylase 1, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 2:10439967-10448327

Links

ENSG00000115758 ∙ NCBI:4953 ∙ OMIM:165640 ∙ HGNC:8109 ∙ Uniprot:P11926 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with alopecia and brain abnormalities (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with alopecia and brain imaging abnormalities (Bachmann-Bupp syndrome)	AD	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	Craniofacial; Dermatologic; Musculoskeletal; Neurologic	30239107; 30475435

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ODC1 gene.

• not provided (27 variants)
• Inborn genetic diseases (9 variants)
• Neurodevelopmental disorder with alopecia and brain abnormalities (5 variants)
• ODC1-related condition (3 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ODC1 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	1	7
missense			28	2	2	32
nonsense						0
start loss						0
frameshift		1	2			3
inframe indel						0
splice donor/acceptor (+/-2bp)	1		2			3
splice region						0
non coding						0
Total	1	1	32	8	3

Variants in ODC1

This is a list of pathogenic ClinVar variants found in the ODC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-10440768-T-A		Neurodevelopmental disorder with alopecia and brain abnormalities	Pathogenic (Jan 05, 2021)
2-10440774-C-T			Likely benign (Sep 01, 2022)
2-10440786-C-T			Uncertain significance (Mar 30, 2023)
2-10440793-CACAG-C		Neurodevelopmental disorder with alopecia and brain abnormalities	Likely pathogenic (Jun 07, 2020)
2-10440798-G-A			Uncertain significance (Mar 29, 2023)
2-10440829-G-A			Likely benign (Feb 01, 2024)
2-10440840-C-T		Neurodevelopmental disorder with alopecia and brain abnormalities	Uncertain significance (Mar 26, 2021)
2-10440841-G-A			Benign (Jun 22, 2018)
2-10440846-TCTGGAATTGCTGCATGAGTTGC-T		Neurodevelopmental disorder with alopecia and brain abnormalities	Pathogenic (Jan 05, 2021)
2-10440855-G-A		Neurodevelopmental disorder with alopecia and brain abnormalities	Pathogenic (Jan 05, 2021)
2-10440870-T-C			Pathogenic (Oct 19, 2020)
2-10441508-C-A		Neurodevelopmental disorder with alopecia and brain abnormalities	Pathogenic (Jan 05, 2021)
2-10441508-C-CCA		Neurodevelopmental disorder with alopecia and brain abnormalities	Pathogenic (Jan 05, 2021)
2-10441512-G-A		Inborn genetic diseases	Uncertain significance (Oct 20, 2023)
2-10441521-G-A			Uncertain significance (Mar 12, 2022)
2-10441533-T-A		ODC1-related disorder	Uncertain significance (Sep 07, 2023)
2-10441539-G-A			Uncertain significance (Nov 03, 2021)
2-10441563-G-A		Neurodevelopmental disorder with alopecia and brain abnormalities	Uncertain significance (Aug 12, 2021)
2-10441588-C-T			Uncertain significance (Apr 19, 2021)
2-10441589-G-A			Likely benign (Apr 01, 2023)
2-10441625-C-T		Inborn genetic diseases	Uncertain significance (Nov 08, 2021)
2-10441644-C-T			Likely benign (Feb 01, 2024)
2-10441645-G-A			Benign (Oct 01, 2022)
2-10441714-G-C		Inborn genetic diseases	Uncertain significance (Jun 22, 2021)
2-10441851-T-TA		ODC1-related disorder	Uncertain significance (Sep 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ODC1	protein_coding	protein_coding	ENST00000234111	10	8537

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.170	0.830	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	209	278	0.752	0.0000157	3064
Missense in Polyphen		41	80.268	0.51079		1027
Synonymous	-0.946	118	106	1.12	0.00000664	862
Loss of Function	3.02	5	19.4	0.258	8.12e-7	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000337	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the first and rate-limiting step of polyamine biosynthesis that converts ornithine into putrescine, which is the precursor for the polyamines, spermidine and spermine. Polyamines are essential for cell proliferation and are implicated in cellular processes, ranging from DNA replication to apoptosis. {ECO:0000269|PubMed:17900240}.
• Pathway: Arginine and proline metabolism - Homo sapiens (human);Glutathione metabolism - Homo sapiens (human);Spermidine and Spermine Biosynthesis;Integrated Breast Cancer Pathway;Methionine De Novo and Salvage Pathway;Amino Acid metabolism;Urea cycle and metabolism of amino groups;Regulation of ornithine decarboxylase (ODC);Metabolism of polyamines;Metabolism of amino acids and derivatives;putrescine biosynthesis I;Metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Arginine Proline metabolism;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

• pRec: 0.398

Intolerance Scores

• loftool: 0.147
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.33

Haploinsufficiency Scores

• pHI: 0.269
• hipred: Y
• hipred_score: 0.654
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Odc1
• Phenotype: embryo phenotype; normal 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); cellular phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: odc1
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: kidney development;regulation of cellular amino acid metabolic process;polyamine metabolic process;positive regulation of cell population proliferation;response to virus;putrescine biosynthetic process from ornithine;regulation of protein catabolic process
• Cellular component: cellular_component;cytoplasm;cytosol;perinuclear region of cytoplasm
• Molecular function: ornithine decarboxylase activity;protein binding;protein homodimerization activity