ODF2L

protein-coding

outer dense fiber of sperm tails 2 like, the group of MicroRNA protein coding host genes

Gene summary

Involved in negative regulation of cilium assembly. Located in centriolar satellite and ciliary basal body. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001366781.1

Inheritance

—

ClinVar variants

U:95B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.9

Max pathogenic AF

—

Genomic locus

chr1:86,346,824-86,396,342

External References & Databases

Ensembl (ENSG00000122417)

Transcript & Mutation Effects

hg38 • Region Span ~49.5 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 ODF2L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 91

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001366781.1. 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		1 clinvar	2
missense			86 clinvar	7 clinvar	2 clinvar	95
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	95	7	3	105

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 92 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001366781.1	RefSeq	NP_001353710.1	16	MANE Select
ENST00000460698.7	Ensembl	ENSP00000433092.2	16	MANE Select
NM_001007022.4	RefSeq	NP_001007023.2	17	Standard
NM_001184765.2	RefSeq	NP_001171694.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell projection organization
negative regulation of cilium assembly

Cellular Component

centrosome
centriole
centriolar satellite
ciliary basal body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359242
Coding exons: 17
Length: 47680
Individuals with no LoFs: 125454
Homozygous LoFs: 0
Heterozygous LoFs: 292
Defined: 125746
p: 0.00116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.204	289	279	1.03	0.0000130	4209
Missense (PolyPhen)		74	75.313	0.98257		1308
Synonymous	-0.385	101	96.2	1.05	0.00000478	1042
Loss of Function	0.529	30	33.3	0.901	0.00000150	510

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00058	0.00055	rare
Latino/Admixed American	0.0018	0.0018	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0.0014	0.0014	notable
European (Non-Finnish)	0.0014	0.0014	notable
South Asian	0.00084	0.00075	rare
Other	0.0012	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a suppressor of ciliogenesis, specifically, the initiation of ciliogenesis. {ECO:0000269|PubMed:28775150}.;

Recessive Scores

pRec: 0.0834

Intolerance Scores

LoFtool: 0.996
RVIS EVS: -0.22
RVIS percentile EVS: 37.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.186

Gene Damage Prediction

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