SPAG11B

sperm associated antigen 11B

Basic information

Region (hg38): 8:7442684-7463674

Links

ENSG00000164871 ∙ NCBI:10407 ∙ OMIM:606560 ∙ HGNC:14534 ∙ Uniprot:Q08648 ∙ 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 SPAG11B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPAG11B 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			5	3		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	3	0

Variants in SPAG11B

This is a list of pathogenic ClinVar variants found in the SPAG11B region.

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

Position	Type	Phenotype	Significance	ClinVar
8-7450775-C-T		not specified	Likely benign (Nov 09, 2021)
8-7462724-C-T		not specified	Uncertain significance (Mar 31, 2024)
8-7462727-G-A		not specified	Uncertain significance (Feb 13, 2024)
8-7462742-C-T		not specified	Uncertain significance (May 04, 2022)
8-7462752-C-T		not specified	Uncertain significance (Sep 25, 2024)
8-7462757-C-T		not specified	Likely benign (Nov 15, 2021)
8-7462785-G-T		not specified	Uncertain significance (Oct 27, 2022)
8-7462856-G-A		not specified	Likely benign (Nov 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPAG11B	protein_coding	protein_coding	ENST00000398462	3	20991

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0278	0.594	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.900	81	61.2	1.32	0.00000344	797
Missense in Polyphen		26	16.513	1.5745		232
Synonymous	0.0649	23	23.4	0.983	0.00000162	243
Loss of Function	0.111	2	2.18	0.919	9.17e-8	36

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	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spag11b

Gene ontology

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