Is there a gene that causes cleft palate puppies?

...and what, as a breeder, you need to know!

Cleft palates are one of those heartbreaking issues that occasionally crop up in breeding, and when they do, it’s natural for questions and speculation to follow. In recent weeks, conversations across the breeding community have reignited an important question

Is there a gene that causes cleft palates in dogs, and can we test for it?

It’s a fair question, and one that deserves a clear, evidence-based answer. As a Breeding Nutritionist who studies both the genetic and nutritional influences behind these developmental conditions, I want to break down what science actually tells us, and how breeders can meaningfully reduce risk through proven, practical steps.

What does the science tell us about genes and clefts? ​🧬

I'm sorry to say... There is no single “cleft-palate gene” that applies across all dog breeds. At present, only two breed-specific genetic variants have been validated in peer-reviewed studies:

1. ADAMTS20: a type of frameshift deletion gene variation which causes cleft lip/palate with syndactyly (CLPS) [1].​
2. DLX6: a type of LINE-1 insertion gene variation which causes cleft palate type 1 (CP1) [1].

​These two gene mutations (defective genes) are autosomal recessive and confined to only Nova Scotia Duck Tolling Retrievers. Commercial DNA test exist for the breed, but no published data confirm either variant exists or causes cleft issues in any other breed of dog.

Even large testing providers state that the ADAMTS20 mutation “has only been documented in the Nova Scotias and is not known to cause clefts in other breeds” [2]. 

So, for breeds such as Cocker Spaniels, Poodles, Dachshunds, Labradors and most others, there is no validated DNA test for cleft-palate risk (AKA proven-by-science-studies way of testing a dog to see if it will produce puppies with cleft palates).

Any claim that a dog is “DNA tested clear for the cleft-palate gene” therefore lacks scientific grounding (outside those two gene variants that exist in the Nova Scotia breed). 

The role of nutrition & maternal environment ​🌱

Nutrition and your girls's environment play a major role in the chance of her having a cleft palate puppy. Even with perfect genetics, correct development depends on the uterine environment during the critical window when the puppy's palate forms (roughly around days 25–35 of gestation).

One nutrient in particular has repeatedly been shown to reduce risk in dogs is folic acid (vitamin B9).

Key literature that every breeder should know about:

• A study in 2005 found that giving 5mg of folic acid per day, from mating, until at least 40 days, saw a 75% reduction of cleft palates in Boston Terriers [3].
• A study in 2013 demonstrated that folic acid supplementation reduced cleft palate cases to just 5% in specifically Pugs & Chihuahuas (both of which are considered highest-risk breeds) [4].
• Major veterinary reproduction textbooks recommend folic acid supplementation during pregnancy in any breeds known to be predisposed to cleft palate (including Canine and Feline Theriogenology by Johnston et al, and Clinical Canine and Feline Reproduction: Evidence-Based Answers by Root Kustritz) [8,9,10]. 

​Folic acid’s role is vital during pregnancy, and it's not just in dogs. It's most mammals. Which is why the UK government fortifies our flour (so this all bakery products e.g. bread, cakes, crackers and everything in between!) to ensure women consume enough Folic Acid to prevent cleft palates, neural-tube and craniofacial defects [6].
​
That public-health policy exists precisely because early folate deficiency is a leading preventable cause of cleft palates!

For breeding dogs, the same applies! Adequate maternal folate levels before and during early gestation are essential to proper midline fusion of the palate.

Are some breeds more likely to have cleft puppies?

Multiple studies identify some of our most loved breeds of dog with higher chances of cleft palate or cleft lip puppies, including [1,5,7]:

• Cocker Spaniels
• Dachshunds
• Beagles
• Bulldogs
  
• Boston Terriers
• Boxers
• Labrador Retrievers
• Miniature Schnauzers
  
• French Bulldogs
• Chihuahuas
• Pekingese and Shih Tzus

These breeds are thought to have craniofacial conformations, genetic predisposition, or developmental pathways that increase susceptibility [1,5,7]. This makes proactive nutritional supplementation particularly valuable.

So, is it just their breed, bad genes and a folic deficiency that causes cleft palates?

While genetics are really important, and do contribute, in most breeds cleft palates are a multifactorial condition. It's not something a simple DNA test can rule out.
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Testing alone does not guarantee freedom from risk, and conversely, a lack of testing does not mean a line is unsafe - far from it. As breeders, our influence lies in controlling the factors we can manage: nutrition, environment, and careful mate selection.
​
Even with excellent management, random developmental variations can still occur. But the data show that folic acid supplementation greatly lowers that likelihood.

Our top tips for avoiding cleft palates...

• Begin folic acid supplementation from the start of her season (or as soon as possible) and continue daily throughout pregnancy. 
• Adjust the dose of folic acid supplementation to match their breed predisposition. 
• Choose the correct design of folic acid - a high-quality, additive-free supplement formulated for dogs.
• Maintain balanced maternal nutrition, minimise stress, avoid teratogenic drugs, and manage temperature during the critical developmental window.
• Keep clear breeding and whelping records to identify any recurrent issues within particular pairings, as clefts can be hereditary. If you have a high cleft incidence from a pairing (following the above tips), it's wise to avoid that pairing in future. 

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We can help!

Our CNC Folic Force supplement is ideal for breeding bitches to support foetal development and reduce the risk of cleft palate and neural-tube defects. We're proud to offer tailored, personalised advice with every order, is precision-dosed and manufactured under GMP-compliance standards, providing the reassurance that your bitch and her puppies have every nutritional advantage.

So...

​There is no universal “cleft-palate gene” that a quick DNA test can clear. Unless you have a Nova Scotia, you cannot DNA test for cleft palate risk.

What is proven through decades of research and even public-health policy in the UK... is... that folic acid saves the lives by reducing the risk of clefts and craniofacial defects in developing puppy embryos.

For breeders, that makes folic acid one of the simplest and most powerful tools available.
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Pair it with a sound, balanced diet, environmental care, and record-keeping, and you’ll be giving every litter the best possible start.

Want to talk through your plans?

Every bitch, breeding line, and environment is different - which means the best prevention plan is one that’s tailored to your situation. If you’d like personal guidance on how to carefully consider cleft-palate risks, balance your girl’s diet, and prepare safely for pregnancy, you can book a 1:1 Breeding Nutrition Coaching Call with me.

Book your call today to feel confident that you’re doing everything possible.

​Further reading & references:

[1] C. Bannasch et al., “Identification of ADAMTS20 and DLX6 variants associated with cleft lip and palate in Nova Scotia Duck Tolling Retrievers,” PLoS Genet., vol. 11, no. 4, e1005059, 2015. doi: 10.1371/journal.pgen.1005059

[2] Embark Vet Support, “Will your test predict the risk of cleft palates?,” 2021 [Online]. Available: https://help.embarkvet.com/hc/en-us/articles/1260804437149

[3] C. M. Elwood, S. Collett, and R. W. Stevens, “Reduction of the incidence of cleft palate in Boston Terriers by oral folic acid supplementation,” Theriogenology, vol. 64, pp. 1618–1622, 2005. doi: 10.1016/j.theriogenology.2005.04.008

[4] N. Domosławska, J. Zduńczyk, and J. Janowski, “Oral folic acid supplementation decreases cleft palate incidence in Pug and Chihuahua dogs,” Bull. Vet. Inst. Pulawy, vol. 57, no. 3, pp. 435–439, 2013.

[5] American College of Veterinary Surgeons (ACVS), “Cleft Palate – Small Animal Surgery,” 2016 [Online]. Available: https://www.acvs.org/small-animal/cleft-palate

[6] UK Government Department of Health and Social Care, “Folic acid fortification of flour to prevent neural tube defects,” Policy Paper, 2023 [Online]. Available: https://www.gov.uk/government/publications/folic-acid-fortification-of-flour
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[7] J. Beever and R. Ellis, “Congenital craniofacial defects in dogs: Pathogenesis and breed predisposition,” Vet. Pathol., vol. 56, no. 5, pp. 727–740, 2019. doi: 10.1177/0300985819854919

[8] M. V. Root Kustritz, Clinical Canine and Feline Reproduction: Evidence-Based Answers. Oxford: Wiley-Blackwell, 2010.
[9] S. D. Johnston, M. V. Root Kustritz, and P. N. S. Olson, Canine and Feline Theriogenology. Philadelphia: Saunders, 2001.
[10] P. W. Concannon, G. C. W. England, J. Verstegen, and C. Linde-Forsberg, Recent Advances in Small Animal Reproduction. Ithaca, NY: International Veterinary Information Service (IVIS), 2009.