SPAG7

sperm associated antigen 7

Basic information

Region (hg38): 17:4959226-4967817

Links

ENSG00000091640 ∙ NCBI:9552 ∙ OMIM:610056 ∙ HGNC:11216 ∙ Uniprot:O75391 ∙ 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 SPAG7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPAG7 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					1	1
missense			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	11	0	2

Variants in SPAG7

This is a list of pathogenic ClinVar variants found in the SPAG7 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4959545-G-A		not specified	Uncertain significance (Feb 06, 2023)
17-4959547-G-A		not specified	Uncertain significance (Sep 18, 2024)
17-4959634-G-A		not specified	Uncertain significance (Jun 22, 2024)
17-4959850-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-4959852-C-T		not specified	Uncertain significance (May 09, 2022)
17-4959858-G-C		not specified	Uncertain significance (Mar 22, 2023)
17-4960038-T-C		not specified	Uncertain significance (Nov 30, 2021)
17-4960072-G-A		not specified	Uncertain significance (Jul 06, 2024)
17-4960115-A-G		not specified	Benign (Mar 29, 2016)
17-4960245-T-C			Benign (Dec 31, 2019)
17-4960279-G-A			Benign (Dec 31, 2019)
17-4960296-C-G		not specified	Uncertain significance (Sep 15, 2021)
17-4960296-C-T		not specified	Uncertain significance (Jun 16, 2024)
17-4960519-T-C		not specified	Uncertain significance (Nov 02, 2023)
17-4960841-C-T		not specified	Uncertain significance (Apr 12, 2023)
17-4960842-G-A		not specified	Uncertain significance (Jul 09, 2021)
17-4967773-G-C		not specified	Uncertain significance (Aug 04, 2023)
17-4967789-C-T		not specified	Uncertain significance (May 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPAG7	protein_coding	protein_coding	ENST00000206020	7	8647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000685	0.923	124805	0	9	124814	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.876	107	136	0.788	0.00000801	1500
Missense in Polyphen		26	36.116	0.71991		428
Synonymous	-1.77	66	50.1	1.32	0.00000288	408
Loss of Function	1.57	7	13.1	0.532	5.67e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000930	0.0000464
European (Non-Finnish)	0.0000532	0.0000530
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.422
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.274
• hipred: N
• hipred_score: 0.349
• ghis: 0.425

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.975

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spag7

Gene ontology

• Cellular component: nucleus
• Molecular function: nucleic acid binding