SPAG4

sperm associated antigen 4, the group of SUN family

Basic information

Region (hg38): 20:35615829-35621094

Links

ENSG00000061656

∙ NCBI:6676 ∙ OMIM:603038 ∙ HGNC:11214 ∙ Uniprot:Q9NPE6 ∙ 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 SPAG4 gene.

not_specified (48 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPAG4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003116.3. 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			47 clinvar	1 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	47	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPAG4	protein_coding	protein_coding	ENST00000374273	12	5158

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.72e-7	0.920	125479	0	269	125748	0.00107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.983	201	244	0.823	0.0000119	2784
Missense in Polyphen		74	91.369	0.8099		1038
Synonymous	0.354	100	105	0.956	0.00000503	884
Loss of Function	1.75	14	23.1	0.607	9.88e-7	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000492	0.000491
Ashkenazi Jewish	0.00	0.00
East Asian	0.0124	0.0124
Finnish	0.0000986	0.0000924
European (Non-Finnish)	0.000197	0.000185
Middle Eastern	0.0124	0.0124
South Asian	0.000229	0.000229
Other	0.000182	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in spermatogenesis. Required for sperm head formation but not required to establish and maintain general polarity of the sperm head. Required for anchoring and organization of the manchette. Required for targeting of SUN3 and probably SYNE1 through a probable SUN1:SYNE3 LINC complex to the nuclear envelope and involved in accurate posterior sperm head localization of the complex. May anchor SUN3 the nuclear envelope. Involved in maintenance of the nuclear envelope integrity. May assist the organization and assembly of outer dense fibers (ODFs), a specific structure of the sperm tail. {ECO:0000250|UniProtKB:O55034, ECO:0000250|UniProtKB:Q9JJF2}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

loftool: 0.781
rvis_EVS: 0.55
rvis_percentile_EVS: 81.48

Haploinsufficiency Scores

pHI: 0.147
hipred: Y
hipred_score: 0.520
ghis: 0.394

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.808

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Spag4
Phenotype: cellular phenotype; reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: nuclear envelope organization;spermatogenesis;cell differentiation;cytoskeletal anchoring at nuclear membrane
Cellular component: nuclear envelope;nuclear inner membrane;cytoplasm;cytoskeleton;integral component of membrane;motile cilium;meiotic nuclear membrane microtubule tethering complex
Molecular function: structural molecule activity;protein binding;protein membrane anchor