SPAG11A

sperm associated antigen 11A

Basic information

Region (hg38): 8:7847876-7868867

Links

ENSG00000178287 ∙ NCBI:653423 ∙ ∙ HGNC:33342 ∙ Uniprot:Q6PDA7 ∙ 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 SPAG11A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPAG11A 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in SPAG11A

This is a list of pathogenic ClinVar variants found in the SPAG11A region.

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

Position	Type	Phenotype	Significance	ClinVar
8-7848765-C-A		not specified	Uncertain significance (Oct 27, 2022)
8-7848792-C-T		not specified	Uncertain significance (Nov 16, 2021)
8-7848798-G-T		not specified	Uncertain significance (May 27, 2022)
8-7848831-C-T		not specified	Uncertain significance (Jun 22, 2021)
8-7848838-A-G		not specified	Uncertain significance (Jun 22, 2021)
8-7860648-G-A			Likely benign (Feb 01, 2023)
8-7860667-G-A		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPAG11A	protein_coding	protein_coding	ENST00000326558	4	20992

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000696	0.172	124260	0	8	124268	0.0000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.142	37	34.7	1.07	0.00000185	654
Missense in Polyphen		10	9.723	1.0285		189
Synonymous	-0.299	12	10.8	1.12	4.96e-7	211
Loss of Function	-1.29	5	2.71	1.84	1.14e-7	58

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000907	0.0000907
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000994	0.00000889
Middle Eastern	0.00	0.00
South Asian	0.000156	0.000133
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have antimicrobial activity. May also play a role sperm maturation, storage, and protection. {ECO:0000250|UniProtKB:Q8VBV2}.

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.178

Gene ontology

• Biological process: defense response to bacterium;antimicrobial humoral immune response mediated by antimicrobial peptide
• Cellular component: extracellular region