SPATA6L

Chr 9

spermatogenesis associated 6 like

Also known as: C9orf68, bA6J24.2

NCBI Gene: 55064 ENSG00000106686 UniProt: Q8N4H0

The protein is predicted to bind myosin light chains and function in spermatogenesis, localizing to the sperm head-tail coupling apparatus. Mutations cause autosomal recessive primary ciliary dyskinesia with severe asthenozoospermia, typically presenting in adulthood with respiratory symptoms and male infertility. The gene is not highly constrained against loss-of-function variants.

ResearchSummary from RefSeq

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]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.74

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.74LOEUF

pLI 0.000

Z-score -0.93

OE 1.24 (0.88–1.74)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-2.46Z-score

OE missense 1.53 (1.38–1.69)

265 obs / 173.7 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.24 (0.88–1.74)

0≤0.351.4

Missense OE?1.53 (1.38–1.69)

0≤0.61.4

Synonymous OE?1.11

0≤1.21.6

LoF obs/exp: 22 / 17.8Missense obs/exp: 265 / 173.7Syn Z: -0.70

Background carrier burden — how many people carry a rare variant somewhere in SPATA6L?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 80

751 rare PASS variants

Rare truncating (LoF)

1 in 1,100

127 rare PASS variants

Rare synonymous (reference)

1 in 360

210 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SPATA6L. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 130	1 in 1,400
South Asian	~43k	1 in 53	1 in 2,200
Remaining (unassigned)	~30k	1 in 53	1 in 600
European (Finnish)	~27k	1 in 890	1 in 650
Admixed American	~22k	1 in 64	1 in 1,200
African / African American	~21k	1 in 44	1 in 260
East Asian	~20k	1 in 78	1 in 600
Ashkenazi Jewish	~13k	1 in 410	none seen
Middle Eastern	~2,884	1 in 46	≈ 1 in 960

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 9 of 11 coding exons well covered in gnomAD exomes; exons 5, 11 marginal. Genomes: all 11.? see exons ↓