SPEF1

sperm flagellar 1

Basic information

Region (hg38): 20:3777504-3781448

Previous symbols: [ "C20orf28" ]

Links

ENSG00000101222 ∙ NCBI:25876 ∙ OMIM:610674 ∙ HGNC:15874 ∙ Uniprot:Q9Y4P9 ∙ 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 SPEF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPEF1 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			21			21
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	0	0

Variants in SPEF1

This is a list of pathogenic ClinVar variants found in the SPEF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-3778249-G-T		not specified	Uncertain significance (Oct 08, 2024)
20-3778295-G-T		not specified	Uncertain significance (Jan 17, 2024)
20-3778306-T-A		not specified	Uncertain significance (Jun 11, 2021)
20-3778312-T-A		not specified	Uncertain significance (Jun 09, 2022)
20-3778752-T-A		not specified	Uncertain significance (Jun 30, 2024)
20-3778777-C-T		not specified	Uncertain significance (Jul 06, 2021)
20-3778972-C-T		not specified	Uncertain significance (May 16, 2024)
20-3778983-G-A		not specified	Uncertain significance (Jan 22, 2025)
20-3778988-C-G		not specified	Uncertain significance (Jan 17, 2024)
20-3779232-C-A		not specified	Uncertain significance (Jun 02, 2023)
20-3779239-T-A		not specified	Uncertain significance (Dec 20, 2022)
20-3779276-C-T		not specified	Uncertain significance (Jun 29, 2023)
20-3779279-C-A		not specified	Uncertain significance (Jun 17, 2024)
20-3779279-C-T		not specified	Uncertain significance (Jul 13, 2022)
20-3779293-T-C		not specified	Uncertain significance (Dec 22, 2023)
20-3779296-G-A		not specified	Uncertain significance (Sep 24, 2024)
20-3779297-C-T		not specified	Uncertain significance (Dec 21, 2022)
20-3779676-C-T		not specified	Uncertain significance (Apr 16, 2024)
20-3781197-G-A		not specified	Uncertain significance (Jan 02, 2024)
20-3781234-G-T		not specified	Uncertain significance (May 15, 2024)
20-3781272-C-T		not specified	Uncertain significance (Nov 12, 2021)
20-3781280-C-G		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPEF1	protein_coding	protein_coding	ENST00000379756	7	3945

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000160	0.676	124792	0	13	124805	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	100	139	0.721	0.00000720	1505
Missense in Polyphen		32	47.33	0.6761		547
Synonymous	1.25	47	59.3	0.793	0.00000322	460
Loss of Function	0.972	9	12.7	0.706	5.91e-7	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000302	0.000287
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000452	0.0000441
Middle Eastern	0.00	0.00
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule-associated protein involved in the stabilization of microtubules along the axis of migration during radial intercalation. Promotes the establishment and stabilization of an axis of microtubules required for the active migration of cells into the outer epithelium (By similarity). Microtubule- associated protein that promotes microtubule bundling and stabilizes microtubules against depolymerization in response to cold shock (By similarity). {ECO:0000250|UniProtKB:Q0IH24, ECO:0000250|UniProtKB:Q99JL1}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.639
• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

• pHI: 0.0949
• hipred: N
• hipred_score: 0.248
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.605

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spef1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: negative regulation of microtubule depolymerization;biological_process;cell migration;cilium-dependent cell motility
• Cellular component: cellular_component;cytoplasm;axoneme;motile cilium
• Molecular function: molecular_function;protein binding;microtubule binding