ODF3L1

outer dense fiber of sperm tails 3 like 1

Basic information

Region (hg38): 15:75724040-75727688

Links

ENSG00000182950 ∙ NCBI:161753 ∙ ∙ HGNC:28735 ∙ Uniprot:Q8IXM7 ∙ 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 ODF3L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ODF3L1 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			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	0

Variants in ODF3L1

This is a list of pathogenic ClinVar variants found in the ODF3L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-75724240-C-A		not specified	Uncertain significance (Jun 22, 2023)
15-75724303-T-A		not specified	Uncertain significance (Sep 22, 2023)
15-75725132-G-A		not specified	Uncertain significance (Feb 09, 2023)
15-75725164-A-C		not specified	Uncertain significance (Feb 27, 2024)
15-75725185-G-A		not specified	Uncertain significance (Aug 08, 2023)
15-75725188-T-C		not specified	Uncertain significance (Dec 15, 2022)
15-75726070-A-G		not specified	Uncertain significance (Dec 13, 2023)
15-75726115-G-A		not specified	Uncertain significance (May 27, 2022)
15-75726138-C-A		not specified	Uncertain significance (Apr 21, 2022)
15-75727091-T-A		not specified	Uncertain significance (Aug 10, 2021)
15-75727122-G-A		not specified	Uncertain significance (Mar 02, 2023)
15-75727131-C-T		not specified	Uncertain significance (Jul 19, 2023)
15-75727182-C-T		not specified	Uncertain significance (Feb 27, 2023)
15-75727202-A-T		not specified	Likely benign (Aug 05, 2023)
15-75727299-T-C		not specified	Uncertain significance (Dec 20, 2023)
15-75727323-C-T		not specified	Likely benign (Feb 22, 2023)
15-75727350-A-T		not specified	Uncertain significance (Nov 08, 2022)
15-75727386-G-A		not specified	Uncertain significance (Mar 07, 2023)
15-75727391-G-C		not specified	Uncertain significance (Mar 02, 2023)
15-75727454-G-A		not specified	Uncertain significance (Mar 03, 2022)
15-75727472-C-T		not specified	Uncertain significance (Dec 27, 2022)
15-75727500-C-T		not specified	Uncertain significance (Jan 26, 2022)
15-75727526-G-A		not specified	Uncertain significance (Oct 12, 2022)
15-75727531-T-G		not specified	Uncertain significance (Sep 01, 2021)
15-75727532-C-T		not specified	Uncertain significance (May 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ODF3L1	protein_coding	protein_coding	ENST00000332145	4	3712

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.57e-10	0.0315	124966	14	768	125748	0.00311

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.442	158	174	0.906	0.0000108	1777
Missense in Polyphen		49	50.535	0.96963		488
Synonymous	0.316	66	69.3	0.952	0.00000431	557
Loss of Function	-0.489	14	12.2	1.15	8.78e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0409	0.0408
Ashkenazi Jewish	0.00	0.00
East Asian	0.00158	0.00158
Finnish	0.00	0.00
European (Non-Finnish)	0.000294	0.000290
Middle Eastern	0.00158	0.00158
South Asian	0.000788	0.000784
Other	0.00164	0.00163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.864
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.3

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.251

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Odf3l1