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.

not_specified (28 variants)

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. These statistics are base on transcript: NM_000015417.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			28 clinvar			28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	28	0	0

Loading clinvar variants...

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