SPATA22

protein-coding

spermatogenesis associated 22

Gene summary

Predicted to be involved in regulation of meiotic cell cycle. Predicted to act upstream of or within several processes, including fertilization; gamete generation; and meiosis I cell cycle process. Predicted to be located in chromosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001170698.2

Inheritance

ClinVar variants

P:5U:47B:5

Top phenotype

Premature ovarian failure 25

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr17:3,440,019-3,513,852

External References & Databases

Ensembl (ENSG00000141255)

Transcript & Mutation Effects

hg38 • Region Span ~73.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

genetic infertilityMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0017143

Submitter: PanelApp Australia

infertility disorderMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0005047

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Premature ovarian failure 25AR

Manifestation: Genitourinary; Obstetric

Intervention: Obstetric

Rationale: Genetic knowledge may be beneficial to allow interventions such as preserving eggs in women with premature ovarian insufficiency

Refs: 34392356; 35285020

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SPATA22 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 51

Premature ovarian failure 25Total: 4

not providedTotal: 3

Spermatogenic failure 96Total: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001170698.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			47 clinvar	4 clinvar		51
nonsense	2 clinvar	1 clinvar				3
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)	1 clinvar					1
Total	4	1	47	5	0	57

Highest pathogenic variant AF is 0.000022315478

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001170698.2	RefSeq	NP_001164169.1	8	MANE Select
ENST00000572969.6	Ensembl	ENSP00000460187.1	8	MANE Select
NM_001170695.2	RefSeq	NP_001164166.1	8	Standard
NM_001170696.2	RefSeq	NP_001164167.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

meiotic DNA repair synthesis
synapsis
gamete generation

Molecular Function

protein binding

Cellular Component

chromosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000573128
Coding exons: 8
Length: 73834
Individuals with no LoFs: 125670
Homozygous LoFs: 0
Heterozygous LoFs: 54
Defined: 125724
p: 0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.291	171	182	0.939	0.00000908	2375
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00040	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00023	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00028	0.00027	rare
South Asian	0.000073	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.138

Gene Damage Prediction

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