BOD1

protein-coding

biorientation of chromosomes in cell division 1

Gene summary

Enables protein phosphatase 2A binding activity and protein phosphatase inhibitor activity. Involved in mitotic sister chromatid biorientation; mitotic sister chromatid cohesion, centromeric; and protein localization to chromosome, centromeric region. Located in centrosome; spindle microtubule; and spindle pole. Part of outer kinetochore. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

FAM44B

MANE transcript

NM_138369.3

Inheritance

ClinVar variants

P:2U:29B:6

Top phenotype

BOD1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr5:173,607,145-173,616,659

External References & Databases

Ensembl (ENSG00000145919)

Transcript & Mutation Effects

hg38 • Region Span ~9.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

intellectual disabilityLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0001071

Submitter: Ambry Genetics

syndromic intellectual disabilityLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0000508

Submitter: Franklin by Genoox

A case report of an affected boy to a consanguineous parents with ID who carried novel homozygous nonsense mutation in BOD1, p.R151X. https://doi.org/10.1111/cge.13799

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BOD1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 23

BOD1-related disorderTotal: 9

not providedTotal: 4

BOD1-related Intellectual DisabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138369.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	5 clinvar		6
missense			25 clinvar			25
nonsense	1 clinvar	1 clinvar				2
start loss						0
frameshift			1 clinvar	1 clinvar		2
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	1	1	29	6	0	37

Highest pathogenic variant AF is 0.00005513929

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138369.3	RefSeq	NP_612378.1	3	MANE Select
ENST00000311086.9	Ensembl	ENSP00000309644.4	3	MANE Select
NM_001159651.3	RefSeq	NP_001153123.1	3	Standard
ENST00000285908.5	Ensembl	ENSP00000285908.5	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

protein phosphatase inhibitor activity
protein phosphatase 2A binding

Cellular Component

spindle pole
condensed chromosome outer kinetochore
cytoplasm
centrosome
spindle microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000311086
Coding exons: 3
Length: 9147
Individuals with no LoFs: 123401
Homozygous LoFs: 0
Heterozygous LoFs: 2347
Defined: 125748
p: 0.00938

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.09	65	94.8	0.685	0.00000458	1178
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.020	0.018	notable
Latino/Admixed American	0.010	0.0098	notable
Ashkenazi Jewish	0.018	0.017	notable
East Asian	0.00011	0.00011	rare
Finnish	0.0097	0.0090	notable
European (Non-Finnish)	0.0087	0.0080	notable
South Asian	0.012	0.012	notable
Other	0.015	0.015	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.773

Gene Damage Prediction

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