ODF3

outer dense fiber of sperm tails 3

Basic information

Region (hg38): 11:196760-200261

Links

ENSG00000177947 ∙ NCBI:113746 ∙ OMIM:608356 ∙ HGNC:19905 ∙ Uniprot:Q96PU9 ∙ 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 ODF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ODF3 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in ODF3

This is a list of pathogenic ClinVar variants found in the ODF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-197309-C-T		not specified	Uncertain significance (May 15, 2024)
11-197345-G-A		not specified	Uncertain significance (Dec 30, 2023)
11-197353-G-C		not specified	Uncertain significance (Dec 01, 2022)
11-197395-C-G		not specified	Uncertain significance (Apr 22, 2022)
11-197640-C-A		not specified	Uncertain significance (Mar 21, 2023)
11-197681-T-G		not specified	Uncertain significance (Aug 08, 2022)
11-197704-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-197725-C-A		not specified	Uncertain significance (May 02, 2024)
11-198236-C-G		not specified	Uncertain significance (Mar 06, 2023)
11-198237-G-A		not specified	Uncertain significance (Nov 21, 2023)
11-198291-A-G		not specified	Uncertain significance (Dec 21, 2021)
11-198297-C-A		not specified	Uncertain significance (Oct 05, 2023)
11-198546-C-G			Likely benign (Nov 01, 2022)
11-198552-C-G		not specified	Uncertain significance (Jul 25, 2023)
11-198571-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-198582-C-G		not specified	Uncertain significance (Apr 25, 2022)
11-199405-C-T		not specified	Uncertain significance (Jan 31, 2024)
11-199983-G-A		not specified	Uncertain significance (Sep 17, 2021)
11-199999-A-G		not specified	Uncertain significance (Mar 16, 2022)
11-200020-T-C		not specified	Uncertain significance (Aug 10, 2021)
11-200029-A-G		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ODF3	protein_coding	protein_coding	ENST00000325113	6	3524

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.147	0.837	125659	0	17	125676	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.437	149	165	0.904	0.0000100	1619
Missense in Polyphen		59	63.562	0.92822		572
Synonymous	0.235	62	64.4	0.963	0.00000397	529
Loss of Function	2.07	3	10.1	0.296	5.14e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000613	0.0000613
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000218
Finnish	0.00	0.00
European (Non-Finnish)	0.0000808	0.0000792
Middle Eastern	0.000218	0.000218
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Outer dense fibers are filamentous structures located on the outside of the axoneme in the midpiece and principal piece of the mammalian sperm tail. May help to maintain the passive elastic structures and elastic recoil of the sperm tail.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.234
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.266

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Odf3

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;cell differentiation
• Cellular component: outer dense fiber;cytoplasm
• Molecular function: protein binding