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

infertility disorder (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Premature ovarian failure 25	AR	Obstetric	Genetic knowledge may be beneficial to allow interventions such as preserving eggs in women with premature ovarian insufficiency	Genitourinary; Obstetric	34392356; 35285020

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. These statistics are base on transcript: . Only rare variants are included in the table.

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 clinvar		1
missense			20 clinvar	2 clinvar		22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	20	3	0

Loading clinvar variants...

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
ghis

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