BOD1

biorientation of chromosomes in cell division 1

Basic information

Region (hg38): 5:173607145-173616659

Previous symbols: [ "FAM44B" ]

Links

ENSG00000145919 ∙ NCBI:91272 ∙ OMIM:616745 ∙ HGNC:25114 ∙ Uniprot:Q96IK1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• syndromic intellectual disability (Limited), mode of inheritance: AR
• intellectual disability (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BOD1 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BOD1 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						0
missense			14			14
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	1	0	14	0	0

Highest pathogenic variant AF is 0.0000131

Variants in BOD1

This is a list of pathogenic ClinVar variants found in the BOD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-173609232-C-T		BOD1-related disorder	Likely benign (Jun 06, 2019)
5-173609241-AG-A		BOD1-related disorder	Likely benign (Apr 01, 2022)
5-173609248-G-A		BOD1-related disorder	Likely benign (May 15, 2019)
5-173609254-A-G		BOD1-related disorder	Likely benign (Oct 17, 2019)
5-173609256-A-T		not specified	Uncertain significance (Jul 19, 2023)
5-173609258-G-A		not specified	Uncertain significance (Jan 31, 2025)
5-173609283-G-C		BOD1-related Intellectual Disability	Uncertain significance (Dec 10, 2021)
5-173609289-G-A		not specified	Uncertain significance (Mar 15, 2024)
5-173609291-G-A		not specified	Uncertain significance (Mar 20, 2024)
5-173609295-G-T		not specified	Uncertain significance (Feb 01, 2025)
5-173609314-T-C		BOD1-related disorder	Likely benign (Apr 10, 2019)
5-173609323-C-T		BOD1-related disorder	Likely benign (Apr 11, 2019)
5-173609324-G-A		not specified	Uncertain significance (Feb 13, 2025)
5-173609339-AT-A		BOD1-related disorder	Uncertain significance (Nov 10, 2023)
5-173609344-T-C		BOD1-related disorder	Likely benign (Jun 21, 2019)
5-173609346-G-A			Likely pathogenic (Nov 22, 2024)
5-173613137-A-G		not specified	Uncertain significance (Apr 06, 2023)
5-173613141-T-A		not specified	Uncertain significance (Dec 03, 2024)
5-173613159-G-A			Pathogenic (Mar 30, 2022)
5-173613179-G-A		not specified	Uncertain significance (May 26, 2024)
5-173613207-G-A		not specified	Uncertain significance (Aug 10, 2024)
5-173613239-A-G		not specified	Uncertain significance (Feb 03, 2025)
5-173613263-G-C			Uncertain significance (Mar 17, 2022)
5-173616313-C-T		not specified	Uncertain significance (Nov 08, 2022)
5-173616343-C-T		not specified	Uncertain significance (Oct 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BOD1	protein_coding	protein_coding	ENST00000311086	3	9147

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.249	0.725	123401	0	2347	125748	0.00938

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	65	94.8	0.685	0.00000458	1178
Missense in Polyphen		6	24.166	0.24828		349
Synonymous	0.184	36	37.4	0.962	0.00000190	385
Loss of Function	1.86	2	7.51	0.266	5.04e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0303	0.0282
Ashkenazi Jewish	0.0176	0.0168
East Asian	0.000109	0.000109
Finnish	0.00971	0.00896
European (Non-Finnish)	0.00867	0.00803
Middle Eastern	0.000109	0.000109
South Asian	0.0122	0.0117
Other	0.0153	0.0146

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for proper chromosome biorientation through the detection or correction of syntelic attachments in mitotic spindles. {ECO:0000269|PubMed:17938248}.

Recessive Scores

• pRec: 0.104

Haploinsufficiency Scores

• pHI: 0.309
• hipred: N
• hipred_score: 0.264
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.773

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bod1

Gene ontology

• Biological process: mitotic metaphase plate congression;negative regulation of phosphoprotein phosphatase activity;cell division;protein localization to chromosome, centromeric region;mitotic sister chromatid cohesion, centromeric;mitotic sister chromatid biorientation
• Cellular component: spindle pole;condensed chromosome outer kinetochore;cytoplasm;centrosome;spindle microtubule
• Molecular function: protein phosphatase inhibitor activity;protein phosphatase 2A binding