ODF2

outer dense fiber of sperm tails 2

Basic information

Region (hg38): 9:128455186-128501292

Links

ENSG00000136811 ∙ NCBI:4957 ∙ OMIM:602015 ∙ HGNC:8114 ∙ Uniprot:Q5BJF6 ∙ 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 ODF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ODF2 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				2		2
missense			28		1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	29	2	1

Variants in ODF2

This is a list of pathogenic ClinVar variants found in the ODF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128456222-G-A		not specified	Uncertain significance (Oct 06, 2021)
9-128459599-G-A		not specified	Uncertain significance (Aug 09, 2021)
9-128459605-C-T		not specified	Uncertain significance (Oct 26, 2021)
9-128459637-G-A		not specified	Uncertain significance (Oct 26, 2021)
9-128460628-A-T		not specified	Uncertain significance (Dec 08, 2023)
9-128460985-G-A		not specified	Uncertain significance (May 06, 2022)
9-128460988-G-A		not specified	Uncertain significance (Apr 20, 2023)
9-128460996-C-T		not specified	Uncertain significance (Sep 27, 2021)
9-128469208-C-T		not specified	Uncertain significance (Nov 07, 2022)
9-128469311-G-T		not specified	Uncertain significance (Jan 27, 2022)
9-128469331-C-T		not specified	Uncertain significance (Apr 07, 2022)
9-128471329-C-G		not specified	Uncertain significance (Oct 17, 2023)
9-128471417-C-T		not specified	Uncertain significance (May 27, 2022)
9-128471437-G-A		not specified	Uncertain significance (Aug 30, 2022)
9-128471441-G-T		not specified	Uncertain significance (Aug 23, 2021)
9-128471475-T-C			Likely benign (Jun 01, 2024)
9-128472947-T-C		not specified	Uncertain significance (Aug 21, 2023)
9-128472972-C-T		not specified	Uncertain significance (Jan 27, 2022)
9-128473041-C-T		not specified	Uncertain significance (Feb 06, 2024)
9-128473637-A-C		not specified	Uncertain significance (Feb 15, 2023)
9-128473701-G-A		not specified	Uncertain significance (Nov 08, 2021)
9-128473703-A-T		not specified	Uncertain significance (Nov 09, 2021)
9-128473710-G-A		not specified	Uncertain significance (Jul 11, 2023)
9-128473713-A-G		not specified	Uncertain significance (Mar 20, 2024)
9-128481647-A-G		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ODF2	protein_coding	protein_coding	ENST00000434106	20	46107

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00124	0.999	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.15	363	498	0.729	0.0000312	5441
Missense in Polyphen		76	111.83	0.67962		1226
Synonymous	0.130	188	190	0.988	0.0000114	1548
Loss of Function	4.57	15	49.8	0.301	0.00000272	570

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000213	0.000193
Middle Eastern	0.000163	0.000163
South Asian	0.000264	0.000261
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to be a major component of sperm tail outer dense fibers (ODF). ODFs are filamentous structures located on the outside of the axoneme in the midpiece and principal piece of the mammalian sperm tail and may help to maintain the passive elastic structures and elastic recoil of the sperm tail. May have a modulating influence on sperm motility. Functions as a general scaffold protein that is specifically localized at the distal/subdistal appendages of mother centrioles. Component of the centrosome matrix required for the localization of PLK1 and NIN to the centrosomes. Required for the formation and/or maintenance of normal CETN1 assembly. {ECO:0000269|PubMed:16966375}.
• Pathway: Regulation of PLK1 Activity at G2/M Transition;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;PLK1 signaling events;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.780
• rvis_EVS: -0.68
• rvis_percentile_EVS: 15.36

Haploinsufficiency Scores

• pHI: 0.514
• hipred: Y
• hipred_score: 0.614
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.600

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Odf2
• Phenotype: growth/size/body region phenotype; cellular phenotype; embryo phenotype; respiratory system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype

Zebrafish Information Network

• Gene name: odf2a
• Affected structure: retina
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;multicellular organism development;spermatid development;protein localization;regulation of G2/M transition of mitotic cell cycle;centriole-centriole cohesion;cilium organization;ciliary basal body-plasma membrane docking
• Cellular component: spindle pole;outer dense fiber;nucleus;centrosome;centriole;cytosol;microtubule;sperm flagellum;ciliary transition fiber;centriolar subdistal appendage
• Molecular function: structural molecule activity;protein binding