ODF2L

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

Basic information

Region (hg38): 1:86346824-86396342

Links

ENSG00000122417 ∙ NCBI:57489 ∙ OMIM:620130 ∙ HGNC:29225 ∙ Uniprot:Q9ULJ1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ODF2L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ODF2L 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					1	1
missense			34	2	2	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	2	3

Variants in ODF2L

This is a list of pathogenic ClinVar variants found in the ODF2L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-86348823-G-A		not specified	Uncertain significance (Jul 09, 2021)
1-86348838-T-C		not specified	Uncertain significance (Oct 12, 2021)
1-86352195-G-A		not specified	Uncertain significance (Mar 20, 2023)
1-86352867-T-C		not specified	Uncertain significance (Feb 28, 2024)
1-86352876-C-A		not specified	Uncertain significance (Apr 20, 2024)
1-86352927-A-T		not specified	Uncertain significance (Dec 31, 2023)
1-86352954-T-C		not specified	Uncertain significance (Sep 16, 2021)
1-86354531-T-G		not specified	Uncertain significance (May 07, 2024)
1-86354816-T-C		not specified	Uncertain significance (Oct 25, 2022)
1-86356479-C-T		not specified	Uncertain significance (May 30, 2023)
1-86356523-T-G		not specified	Uncertain significance (Jan 03, 2024)
1-86356543-C-T			Benign (Dec 31, 2019)
1-86356562-C-T			Benign (Jun 26, 2018)
1-86356585-C-A		not specified	Uncertain significance (Jan 04, 2022)
1-86358813-T-C			Benign (Aug 30, 2018)
1-86358880-C-A		not specified	Uncertain significance (Feb 10, 2023)
1-86360428-G-C		not specified	Uncertain significance (May 30, 2024)
1-86360451-G-T		not specified	Uncertain significance (Feb 28, 2023)
1-86360459-T-A		not specified	Likely benign (May 23, 2024)
1-86360466-T-C		not specified	Uncertain significance (Dec 12, 2023)
1-86360511-T-C		not specified	Uncertain significance (Mar 30, 2024)
1-86371029-T-C		not specified	Uncertain significance (May 28, 2024)
1-86371038-G-C		not specified	Uncertain significance (Dec 27, 2023)
1-86371047-T-C		not specified	Uncertain significance (Nov 30, 2021)
1-86371094-C-A		not specified	Uncertain significance (Nov 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ODF2L	protein_coding	protein_coding	ENST00000359242	17	47680

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.67e-19	0.0121	125454	0	292	125746	0.00116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.204	289	279	1.03	0.0000130	4209
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00243	0.00240
Ashkenazi Jewish	0.00	0.00
East Asian	0.000328	0.000326
Finnish	0.00139	0.00139
European (Non-Finnish)	0.00136	0.00135
Middle Eastern	0.000328	0.000326
South Asian	0.000841	0.000752
Other	0.00115	0.00114

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0909
• hipred: N
• hipred_score: 0.146
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.186

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Odf2l

Gene ontology

• Biological process: cell projection organization;negative regulation of cilium assembly
• Cellular component: centrosome;centriole;centriolar satellite;ciliary basal body