ODF3B

outer dense fiber of sperm tails 3B

Basic information

Region (hg38): 22:50529709-50532506

Links

ENSG00000177989 ∙ NCBI:440836 ∙ ∙ HGNC:34388 ∙ Uniprot:A8MYP8 ∙ 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 ODF3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ODF3B 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in ODF3B

This is a list of pathogenic ClinVar variants found in the ODF3B region.

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

Position	Type	Phenotype	Significance	ClinVar
22-50529713-T-C		TYMP-related disorder	Uncertain significance (Feb 01, 2017)
22-50529755-C-A		not specified	Likely benign (Jul 07, 2017)
22-50529836-T-G			Benign (Jul 07, 2018)
22-50529913-G-A		Mitochondrial DNA depletion syndrome 1	Uncertain significance (Apr 27, 2017)
22-50529977-A-G		Mitochondrial DNA depletion syndrome 1	Uncertain significance (Jan 13, 2018)
22-50529985-G-A		Mitochondrial DNA depletion syndrome 1	Uncertain significance (Jan 13, 2018)
22-50530043-G-C		Mitochondrial DNA depletion syndrome 1	Uncertain significance (Jan 13, 2018)
22-50530129-C-T			Benign (Jun 14, 2018)
22-50530509-C-T		not specified	Uncertain significance (Sep 18, 2023)
22-50530559-T-C		not specified	Uncertain significance (Dec 17, 2021)
22-50530743-T-G		not specified	Uncertain significance (Feb 27, 2024)
22-50530791-T-C		not specified	Uncertain significance (May 18, 2023)
22-50530951-C-G		not specified	Uncertain significance (Jan 10, 2022)
22-50530959-C-G		not specified	Uncertain significance (Jan 31, 2024)
22-50531049-G-A		not specified	Uncertain significance (Dec 19, 2022)
22-50531208-G-A		not specified	Uncertain significance (Nov 07, 2022)
22-50531208-G-T		not specified	Uncertain significance (May 08, 2023)
22-50531247-G-A		not specified	Uncertain significance (Jan 23, 2024)
22-50531768-C-T		not specified	Uncertain significance (Apr 05, 2023)
22-50531980-G-T		not specified	Uncertain significance (Oct 26, 2022)
22-50532004-C-A		not specified	Uncertain significance (Aug 02, 2021)
22-50532010-T-C		not specified	Uncertain significance (Feb 26, 2024)
22-50532068-C-T		not specified	Uncertain significance (Jan 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ODF3B	protein_coding	protein_coding	ENST00000329363	6	2871

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00455	0.885	124309	0	18	124327	0.0000724

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.893	91	118	0.769	0.00000550	1550
Missense in Polyphen		22	45.869	0.47963		610
Synonymous	0.155	52	53.4	0.973	0.00000271	555
Loss of Function	1.35	5	9.51	0.526	4.60e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000139	0.000130
Ashkenazi Jewish	0.00	0.00
East Asian	0.000337	0.000334
Finnish	0.0000471	0.0000464
European (Non-Finnish)	0.0000756	0.0000711
Middle Eastern	0.000337	0.000334
South Asian	0.0000343	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.314
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.471

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Odf3b