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.

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.

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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in SPAG4

This is a list of pathogenic ClinVar variants found in the SPAG4 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-35616035-C-T		not specified	Uncertain significance (Nov 22, 2021)
20-35616055-C-T		not specified	Uncertain significance (Jun 29, 2023)
20-35616070-G-A		not specified	Uncertain significance (Jun 10, 2024)
20-35616083-T-G		not specified	Uncertain significance (Sep 30, 2024)
20-35616115-C-T		not specified	Uncertain significance (Feb 08, 2025)
20-35616142-C-T		not specified	Uncertain significance (Mar 12, 2024)
20-35616163-G-A		not specified	Uncertain significance (Jul 19, 2022)
20-35616260-A-G		not specified	Uncertain significance (May 18, 2023)
20-35617184-C-T		not specified	Uncertain significance (Feb 19, 2025)
20-35617220-G-C		not specified	Uncertain significance (Aug 10, 2021)
20-35617540-A-G		not specified	Uncertain significance (Jul 30, 2024)
20-35617541-G-A		not specified	Uncertain significance (Jul 30, 2024)
20-35617580-T-C		not specified	Uncertain significance (Dec 09, 2023)
20-35618087-C-T		not specified	Uncertain significance (Jul 13, 2022)
20-35618625-C-T		not specified	Uncertain significance (Aug 28, 2024)
20-35618655-C-A		not specified	Uncertain significance (Jul 30, 2024)
20-35618697-A-T		not specified	Likely benign (Dec 04, 2024)
20-35618938-G-T		not specified	Uncertain significance (Feb 15, 2025)
20-35618979-C-G		not specified	Uncertain significance (Oct 05, 2023)
20-35619198-C-T		not specified	Uncertain significance (Jun 02, 2023)
20-35619607-C-T		not specified	Uncertain significance (Nov 13, 2024)
20-35619609-T-A		not specified	Uncertain significance (Jun 16, 2023)
20-35619694-G-A		not specified	Uncertain significance (Nov 17, 2023)
20-35619695-C-A		not specified	Uncertain significance (Jul 26, 2024)
20-35619732-G-A		not specified	Uncertain significance (Oct 29, 2024)

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