ODF4

outer dense fiber of sperm tails 4

Basic information

Region (hg38): 17:8339839-8346048

Links

ENSG00000184650 ∙ NCBI:146852 ∙ OMIM:610097 ∙ HGNC:19056 ∙ Uniprot:Q2M2E3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ODF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ODF4 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						0
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in ODF4

This is a list of pathogenic ClinVar variants found in the ODF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-8340086-G-A		not specified	Uncertain significance (Sep 29, 2023)
17-8340105-C-A		not specified	Uncertain significance (Dec 16, 2022)
17-8340106-C-A		not specified	Uncertain significance (Dec 16, 2022)
17-8340136-A-T		not specified	Uncertain significance (Feb 02, 2024)
17-8340232-C-T		not specified	Uncertain significance (Jun 11, 2024)
17-8340239-A-C		not specified	Uncertain significance (Mar 18, 2024)
17-8340482-G-A		not specified	Uncertain significance (Jun 17, 2022)
17-8345346-C-T		not specified	Uncertain significance (Feb 28, 2023)
17-8345423-A-G		not specified	Uncertain significance (May 06, 2024)
17-8345686-A-T		not specified	Uncertain significance (Apr 12, 2024)
17-8345776-G-C		not specified	Uncertain significance (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ODF4	protein_coding	protein_coding	ENST00000328248	3	6183

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0108	0.847	125732	0	2	125734	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.927	110	141	0.780	0.00000715	1695
Missense in Polyphen		21	31.672	0.66304		418
Synonymous	0.790	50	57.6	0.868	0.00000304	499
Loss of Function	1.19	4	7.52	0.532	3.19e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the outer dense fibers (ODF) of spermatozoa which could be involved in sperm tail structure, sperm movement and general organization of cellular cytoskeleton. {ECO:0000250}.

Recessive Scores

• pRec: 0.0842

Intolerance Scores

• loftool: 0.802
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.44

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.191

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Odf4

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;cell differentiation
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding