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_specified (21 variants)
• BOD1-related_disorder (8 variants)
• not_provided (3 variants)
• BOD1-related_Intellectual_Disability (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. These statistics are base on transcript: NM_000138369.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5		5
missense			22			22
nonsense	1	1				2
start loss						0
frameshift			1	1		2
splice donor/acceptor (+/-2bp)						0
Total	1	1	23	6	0

Highest pathogenic variant AF is 0.00005513929

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