BOD1L1

protein-coding

biorientation of chromosomes in cell division 1 like 1

Gene summary

Involved in DNA damage response and replication fork processing. Predicted to be located in nucleoplasm. Predicted to be part of Set1C/COMPASS complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

FAM44A
BOD1L

MANE transcript

NM_148894.3

Inheritance

—

ClinVar variants

U:438B:39

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr4:13,568,738-13,627,725

External References & Databases

Ensembl (ENSG00000038219)

Transcript & Mutation Effects

hg38 • Region Span ~59.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BOD1L1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 439

not providedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_148894.3. 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			7 clinvar	2 clinvar		9
missense			417 clinvar	37 clinvar		454
nonsense			5 clinvar			5
start loss						0
frameshift			5 clinvar			5
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	438	39	0	477

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_148894.3	RefSeq	NP_683692.2	26	MANE Select
ENST00000040738.10	Ensembl	ENSP00000040738.5	26	MANE Select
ENST00000482713.1	Ensembl	ENSP00000420541.1	2	Standard
ENST00000507943.2	Ensembl	ENSP00000425492.2	27	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

DNA repair
cellular response to DNA damage stimulus
replication fork processing

Cellular Component

nucleoplasm
chromosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000040738
Coding exons: 26
Length: 58986
Individuals with no LoFs: 125559
Homozygous LoFs: 0
Heterozygous LoFs: 34
Defined: 125593
p: 0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.666	1425	1.50e+3	0.952	0.0000751	20072
Missense (PolyPhen)		316	401.19	0.78765		5651
Synonymous	-0.518	557	542	1.03	0.0000295	5783
Loss of Function	7.55	16	95.7	0.167	0.00000479	1545

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000095	0.000092	rare
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.00013	0.00013	rare
Other	0.00035	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the fork protection machinery required to protect stalled/damaged replication forks from uncontrolled DNA2- dependent resection. Acts by stabilizing RAD51 at stalled replication forks and protecting RAD51 nucleofilaments from the antirecombinogenic activities of FBH1 and BLM (PubMed:26166705). Does not regulate spindle orientation (PubMed:26166705). {ECO:0000269|PubMed:26166705}.;

Recessive Scores

pRec: 0.0892

Intolerance Scores

RVIS EVS: -0.63
RVIS percentile EVS: 16.79

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E

Gene Damage Prediction

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