SPATA6L

protein-coding

spermatogenesis associated 6 like

Gene summary

Predicted to enable myosin light chain binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in sperm head-tail coupling apparatus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C9orf68

MANE transcript

NM_001353486.2

Inheritance

—

ClinVar variants

U:72B:4

Top phenotype

PLPP6-related disorder

gnomAD constraint

pLI —, LoF o/e 1.24

Max pathogenic AF

—

Genomic locus

chr9:4,553,386-4,666,674

External References & Databases

Ensembl (ENSG00000106686)

Transcript & Mutation Effects

hg38 • Region Span ~113.3 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 SPATA6L variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 125

PLPP6-related disorderTotal: 7

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001353486.2. 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			70 clinvar	3 clinvar		73
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	72	4	0	76

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001353486.2	RefSeq	NP_001340415.1	11	MANE Select
ENST00000682582.1	Ensembl	ENSP00000506787.1	11	MANE Select
NM_001039395.4	RefSeq	NP_001034484.3	9	Standard
NM_001353484.2	RefSeq	NP_001340413.1	12	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000475086
Coding exons: 9
Length: 113289
Individuals with no LoFs: 124742
Homozygous LoFs: 0
Heterozygous LoFs: 52
Defined: 124794
p: 0.000208

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.46	265	174	1.53	0.00000835	2184
Missense (PolyPhen)		124	82.675	1.4999		1109
Synonymous	-0.696	72	64.9	1.11	0.00000323	627
Loss of Function	-0.932	22	17.8	1.24	8.43e-7	233

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0016	0.0016	notable
Latino/Admixed American	0.00026	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00028	rare
Finnish	0.000095	0.000093	rare
European (Non-Finnish)	0.000097	0.000097	rare
South Asian	0.000067	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1.22
RVIS percentile EVS: 93.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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