ODF3L2

outer dense fiber of sperm tails 3 like 2

Basic information

Region (hg38): 19:463345-474983

Previous symbols: [ "C19orf19" ]

Links

ENSG00000181781 ∙ NCBI:284451 ∙ ∙ HGNC:26841 ∙ Uniprot:Q3SX64 ∙ 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 ODF3L2 gene.

• Inborn genetic diseases (22 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ODF3L2 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in ODF3L2

This is a list of pathogenic ClinVar variants found in the ODF3L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-463863-A-C		not specified	Uncertain significance (Nov 21, 2023)
19-463882-G-C		not specified	Uncertain significance (Jan 06, 2023)
19-463914-C-T		not specified	Uncertain significance (Aug 03, 2022)
19-463934-C-T		not specified	Uncertain significance (May 31, 2023)
19-464022-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-464029-G-A		not specified	Uncertain significance (Aug 16, 2021)
19-464032-G-A		not specified	Uncertain significance (Jan 07, 2022)
19-464034-C-T		not specified	Uncertain significance (Feb 22, 2023)
19-464035-G-A		not specified	Uncertain significance (Dec 12, 2023)
19-464047-T-C		not specified	Uncertain significance (Nov 27, 2023)
19-464062-G-A		not specified	Uncertain significance (May 17, 2023)
19-464067-C-T		not specified	Uncertain significance (Jan 10, 2023)
19-464068-G-A		not specified	Uncertain significance (Jan 30, 2024)
19-464103-G-A		not specified	Uncertain significance (Jan 18, 2022)
19-464113-T-A		not specified	Uncertain significance (Aug 08, 2023)
19-464125-C-G		not specified	Uncertain significance (Oct 04, 2022)
19-464140-C-T		not specified	Likely benign (Aug 02, 2021)
19-464142-G-C		not specified	Uncertain significance (Feb 16, 2023)
19-464143-G-A		not specified	Uncertain significance (Apr 07, 2022)
19-464143-G-C		not specified	Uncertain significance (Sep 26, 2023)
19-464145-G-A		not specified	Uncertain significance (Dec 27, 2023)
19-464163-G-A		not specified	Uncertain significance (Jan 18, 2022)
19-464254-G-T		not specified	Uncertain significance (Jul 17, 2023)
19-464271-C-T		not specified	Uncertain significance (Sep 01, 2021)
19-464292-G-A		not specified	Uncertain significance (Jan 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ODF3L2	protein_coding	protein_coding	ENST00000315489	4	11638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0256	0.798	125089	0	4	125093	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.113	166	170	0.976	0.0000118	1774
Missense in Polyphen		44	54.665	0.8049		543
Synonymous	-0.189	76	73.9	1.03	0.00000512	660
Loss of Function	1.01	3	5.58	0.538	2.35e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000985	0.0000985
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000164

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.131
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.220

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Odf3l2
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hearing/vestibular/ear phenotype

Gene ontology

• Cellular component: cytoplasmic microtubule