SPATA20

protein-coding

spermatogenesis associated 20

Gene summary

Predicted to be involved in carbohydrate metabolic process; cell differentiation; and spermatogenesis. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_022827.4

Inheritance

—

ClinVar variants

U:155B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.49

Max pathogenic AF

—

Genomic locus

chr17:50,543,058-50,555,852

External References & Databases

Ensembl (ENSG00000006282)

Transcript & Mutation Effects

hg38 • Region Span ~12.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SPATA20 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 151

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022827.4. 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			2 clinvar	1 clinvar		3
missense			148 clinvar	5 clinvar		153
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	155	6	0	161

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 96 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022827.4	RefSeq	NP_073738.2	17	MANE Select
ENST00000006658.11	Ensembl	ENSP00000006658.6	17	MANE Select
NM_001258372.2	RefSeq	NP_001245301.1	16	Standard
NM_001258373.2	RefSeq	NP_001245302.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

multicellular organism development
spermatogenesis
cell differentiation

Molecular Function

catalytic activity

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000006658
Coding exons: 17
Length: 12795
Individuals with no LoFs: 125515
Homozygous LoFs: 0
Heterozygous LoFs: 233
Defined: 125748
p: 0.000927

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.123	490	498	0.985	0.0000326	5156
Missense (PolyPhen)		154	164.39	0.93681		1727
Synonymous	0.417	200	208	0.963	0.0000136	1644
Loss of Function	3.18	22	45.0	0.489	0.00000244	456

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0079	0.0078	notable
Latino/Admixed American	0.00076	0.00067	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00056	0.00055	rare
South Asian	0.00029	0.00029	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in fertility regulation. {ECO:0000250}.;

Recessive Scores

pRec: 0.155

Intolerance Scores

LoFtool: 0.722
RVIS EVS: -0.59
RVIS percentile EVS: 18.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.517

Gene Damage Prediction

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