ODF1

outer dense fiber of sperm tails 1, the group of Small heat shock proteins

Basic information

Region (hg38): 8:102551589-102561018

Links

ENSG00000155087 ∙ NCBI:4956 ∙ OMIM:182878 ∙ HGNC:8113 ∙ Uniprot:Q14990 ∙ 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 ODF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ODF1 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			19			19
nonsense						0
start loss						0
frameshift					2	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	3

Variants in ODF1

This is a list of pathogenic ClinVar variants found in the ODF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-102551771-T-C		not specified	Uncertain significance (Jun 28, 2024)
8-102551815-G-A		not specified	Uncertain significance (May 27, 2022)
8-102551839-G-A		not specified	Uncertain significance (Dec 21, 2023)
8-102551909-G-A		not specified	Uncertain significance (Jul 14, 2021)
8-102551914-C-T		not specified	Uncertain significance (Jun 12, 2023)
8-102551942-C-T		not specified	Uncertain significance (Nov 26, 2024)
8-102551995-T-G		not specified	Uncertain significance (Aug 10, 2021)
8-102552003-G-T		not specified	Uncertain significance (Jan 11, 2023)
8-102552019-A-C		not specified	Uncertain significance (Jun 30, 2022)
8-102552035-G-A		not specified	Uncertain significance (Jun 23, 2023)
8-102560468-A-G		not specified	Uncertain significance (Mar 04, 2024)
8-102560472-G-T		not specified	Uncertain significance (May 31, 2022)
8-102560489-T-C		not specified	Uncertain significance (May 31, 2023)
8-102560492-T-A		not specified	Uncertain significance (Feb 17, 2024)
8-102560528-G-A		not specified	Uncertain significance (Aug 02, 2022)
8-102560540-G-A		not specified	Uncertain significance (Jan 31, 2024)
8-102560592-G-A		not specified	Uncertain significance (Feb 10, 2023)
8-102560594-G-A		not specified	Uncertain significance (May 23, 2024)
8-102560708-G-A		not specified	Uncertain significance (Sep 22, 2023)
8-102560773-C-G			Benign (Aug 20, 2018)
8-102560795-AGCCCCTGC-A			Benign (Aug 20, 2018)
8-102560804-AACCCGTGCAG-A			Benign (Aug 20, 2018)
8-102560808-C-T		not specified	Uncertain significance (Sep 01, 2021)
8-102560865-G-T		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ODF1	protein_coding	protein_coding	ENST00000285402	2	9446

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.972	0.0279	124825	15	793	125633	0.00322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.680	123	146	0.842	0.00000825	1629
Missense in Polyphen		37	51.25	0.72195		562
Synonymous	0.435	57	61.3	0.929	0.00000394	461
Loss of Function	3.08	0	11.0	0.00	7.79e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.110	0.0485
Ashkenazi Jewish	0.00	0.00
East Asian	0.000270	0.000109
Finnish	0.000111	0.0000462
European (Non-Finnish)	0.000607	0.000264
Middle Eastern	0.000270	0.000109
South Asian	0.000231	0.0000980
Other	0.00466	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the outer dense fibers (ODF) of spermatozoa. ODF 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.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.435
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.496
• hipred: Y
• hipred_score: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.496

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Odf1
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

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