SPATA22

spermatogenesis associated 22

Basic information

Region (hg38): 17:3440019-3513852

Links

ENSG00000141255 ∙ NCBI:84690 ∙ OMIM:617673 ∙ HGNC:30705 ∙ Uniprot:Q8NHS9 ∙ 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 SPATA22 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA22 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			16	2		18
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	16	3	0

Variants in SPATA22

This is a list of pathogenic ClinVar variants found in the SPATA22 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-3440172-T-C		not specified	Uncertain significance (May 05, 2023)
17-3440241-G-A		not specified	Uncertain significance (Jan 31, 2024)
17-3440324-C-T			Likely benign (Jun 01, 2022)
17-3446513-C-T		not specified	Uncertain significance (Jun 11, 2021)
17-3446526-T-A		not specified	Uncertain significance (May 04, 2022)
17-3446535-T-C		not specified	Uncertain significance (Jan 16, 2024)
17-3448892-G-A		not specified	Uncertain significance (Jan 31, 2024)
17-3448905-C-T		not specified	Uncertain significance (Jan 10, 2022)
17-3448917-T-C		not specified	Uncertain significance (Jul 17, 2023)
17-3449127-T-C		not specified	Uncertain significance (Dec 11, 2023)
17-3462507-G-C		not specified	Uncertain significance (Jul 20, 2021)
17-3462522-G-C		not specified	Uncertain significance (Dec 18, 2023)
17-3462558-GA-G			Uncertain significance (Jun 04, 2024)
17-3462699-C-T			Uncertain significance (Feb 01, 2024)
17-3462717-C-T		not specified	Likely benign (Nov 09, 2021)
17-3467438-G-A		not specified	Uncertain significance (Dec 02, 2022)
17-3467452-T-C		not specified	Likely benign (Aug 23, 2021)
17-3467464-G-A		not specified	Uncertain significance (Dec 09, 2023)
17-3467539-G-A		not specified	Uncertain significance (Jan 04, 2024)
17-3467540-G-A		not specified	Uncertain significance (Nov 08, 2022)
17-3469285-G-T		not specified	Uncertain significance (Oct 26, 2022)
17-3476008-C-T		Spongy degeneration of central nervous system	Uncertain significance (Jun 14, 2016)
17-3476055-T-C		Spongy degeneration of central nervous system	Uncertain significance (Jun 14, 2016)
17-3476154-G-A		Spongy degeneration of central nervous system	Uncertain significance (Jul 14, 2021)
17-3476161-T-C		Spongy degeneration of central nervous system	Pathogenic/Likely pathogenic (May 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA22	protein_coding	protein_coding	ENST00000573128	8	73834

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000425	0.992	125670	0	54	125724	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.291	171	182	0.939	0.00000908	2375
Missense in Polyphen		44	52.427	0.83926		730
Synonymous	-0.328	65	61.7	1.05	0.00000306	664
Loss of Function	2.35	9	20.5	0.439	0.00000118	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000529	0.000528
Ashkenazi Jewish	0.00	0.00
East Asian	0.000231	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000284	0.000273
Middle Eastern	0.000231	0.000217
South Asian	0.0000734	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Meiosis-specific protein required for homologous recombination in meiosis I. {ECO:0000250}.

Recessive Scores

• pRec: 0.0810

Intolerance Scores

• loftool: 0.897
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.92

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.173

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.138

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata22
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype; skeleton phenotype

Gene ontology

• Biological process: meiotic DNA repair synthesis;synapsis;gamete generation
• Cellular component: chromosome
• Molecular function: protein binding