SPATA21

spermatogenesis associated 21, the group of EF-hand domain containing

Basic information

Region (hg38): 1:16387117-16437424

Links

ENSG00000187144 ∙ NCBI:374955 ∙ ∙ HGNC:28026 ∙ Uniprot:Q7Z572 ∙ 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 SPATA21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA21 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			28	4		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	28	5	0

Variants in SPATA21

This is a list of pathogenic ClinVar variants found in the SPATA21 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-16398827-GGA-G			Benign (May 30, 2017)
1-16399419-A-G		not specified	Uncertain significance (Feb 06, 2024)
1-16399422-G-A		not specified	Likely benign (Jan 03, 2024)
1-16399437-G-A		not specified	Uncertain significance (Aug 21, 2024)
1-16400741-G-A		not specified	Uncertain significance (Oct 11, 2024)
1-16400753-T-A		not specified	Uncertain significance (Mar 06, 2023)
1-16400765-G-C		not specified	Uncertain significance (Oct 25, 2022)
1-16400797-G-T		not specified	Uncertain significance (Jan 17, 2024)
1-16400798-G-A		not specified	Uncertain significance (Apr 06, 2023)
1-16400799-G-T		not specified	Uncertain significance (Aug 02, 2022)
1-16400801-T-C		not specified	Uncertain significance (Dec 03, 2021)
1-16400806-G-A		not specified	Uncertain significance (Jul 09, 2024)
1-16400821-C-T		not specified	Uncertain significance (Oct 29, 2024)
1-16400863-G-C		not specified	Uncertain significance (Aug 27, 2024)
1-16400892-G-C		not specified	Uncertain significance (Feb 06, 2023)
1-16403728-T-C		not specified	Uncertain significance (Jun 14, 2022)
1-16403739-T-C		not specified	Uncertain significance (Apr 07, 2022)
1-16403799-A-T		not specified	Uncertain significance (Dec 06, 2024)
1-16403824-T-C		not specified	Uncertain significance (Jun 09, 2022)
1-16405023-C-A		not specified	Uncertain significance (Oct 24, 2023)
1-16405093-A-C		not specified	Uncertain significance (Mar 22, 2023)
1-16405096-T-C		not specified	Uncertain significance (Apr 25, 2022)
1-16409157-C-G		not specified	Uncertain significance (Dec 28, 2023)
1-16409159-C-T		not specified	Uncertain significance (Apr 11, 2023)
1-16409629-C-T		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA21	protein_coding	protein_coding	ENST00000335496	11	50308

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.13e-17	0.00268	125647	0	99	125746	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00793	274	274	1.00	0.0000161	3022
Missense in Polyphen		37	47.332	0.78171		643
Synonymous	-0.806	121	110	1.10	0.00000652	933
Loss of Function	-0.328	25	23.3	1.07	0.00000109	271

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00117	0.00116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000935	0.000925
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000313	0.000308
Middle Eastern	0.000935	0.000925
South Asian	0.000335	0.000327
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the differentiation of haploid spermatids. {ECO:0000250}.

Intolerance Scores

• loftool: 0.882
• rvis_EVS: 1.31
• rvis_percentile_EVS: 94.04

Haploinsufficiency Scores

• pHI: 0.618
• hipred: N
• hipred_score: 0.112
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0665

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata21

Gene ontology

• Molecular function: calcium ion binding