SPATA2L

protein-coding

spermatogenesis associated 2 like

Gene summary

Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C16orf76

MANE transcript

NM_152339.4

Inheritance

—

ClinVar variants

U:78B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr16:89,696,357-89,701,705

External References & Databases

Ensembl (ENSG00000158792)

Transcript & Mutation Effects

hg38 • Region Span ~5.3 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 SPATA2L variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 78

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152339.4. 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						0
missense			77 clinvar	2 clinvar		79
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	78	2	0	80

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152339.4	RefSeq	NP_689552.2	2	MANE Select
ENST00000289805.10	Ensembl	ENSP00000289805.5	2	MANE Select
ENST00000335360.11	Ensembl	ENSP00000334006.7	3	Standard
ENST00000335360.12	Ensembl	ENSP00000334006.7	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Necroptosis - Homo sapiens (human)

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000289805
Coding exons: 2
Length: 5363
Individuals with no LoFs: 125458
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125475
p: 0.0000677

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.256	265	254	1.05	0.0000163	2602
Missense (PolyPhen)		59	81.393	0.72488		944
Synonymous	-3.26	161	116	1.38	0.00000747	968
Loss of Function	1.92	4	10.8	0.370	5.44e-7	122

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00018	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.110

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.901

Gene Damage Prediction

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