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Alkuraya-Kucinskas Syndrome and Related Disorders via the BLTP1/KIAA1109 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
BLTP1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
6979BLTP181479 81479,81479 $990 Order Options and Pricing

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Angela Gruber, PhD

Clinical Features and Genetics

Clinical Features

Alkuraya-Kucinskas syndrome has been reported in over ten families. Brain malformations and arthrogryposis are hallmark features (Kumar et al. 2020. PubMed ID: 32590954; Gueneau et al. 2018. PubMed ID: 29290337; Filatova et al. 2019. PubMed ID: 30485398; Guo et al. 2020. PubMed ID: 31680349). In the largest cohort study, 11 of 13 individuals presented with hydrocephaly or ventriculomegaly, 8 of 13 presented with corpus callosum agenesis, 10 of 13 presented with arthrogryposis or contractures, 12 of 13 presented with club foot, and 6 of 13 presented with heart defects (Gueneau et al. 2018. PubMed ID: 29290337). Minor features can include retrognathia, low set ears, high arched palate, webbed neck, renal defects, ophthalmoplegic defects, and neonatal breathing difficulties. Loss of function variants result in a more severe clinical presentation that is detected on a prenatal ultrasound and typically results in fetal demise or neonatal death. Individuals with bi-allelic missense variants exhibit a less severe phenotype that includes global developmental delay, mild to moderate learning disability, lack of speech, muscle hypotonia, stereotypic movements, dysmorphic features, and early-onset epilepsy. In some causes only mild intellectual disability and delayed motor milestones were noted, indicating a wide phenotypic spectrum for this disorder (Kumar et al. 2020. PubMed ID: 32590954). Genetic testing may aid in establishing a differential diagnosis and may assist reproductive planning.


Pathogenic variants in BLTP1/KIAA1109 are associated with autosomal recessive Alkuraya-Kucinskas syndrome. Reported variants include missense; nonsense; splicing; small, frameshifting deletions and duplications; and one large intragenic deletion. Loss of function variants result in a more severe phenotype, while missense variants can result in a much milder phenotype of intellectual disability and motor delays. All reported variants were inherited from a carrier parent. BLTP1 is relatively intolerant to missense variants (Genome Aggregation Database).

BLTP1 encodes a large protein (5005 amino acids) that has no known functional domains or motifs and remains functionally uncharacterized. Some studies on this gene suggest it has a possible role in embryonic development and regulation of phagocytosis (Kumar et al. 2020. PubMed ID: 32590954). The fruit fly ortholog, Tweek, is involved in synaptic vesicle recycling which may suggest a role in brain-related functions (Verstreken et al. 2009. PubMed ID: 19640479). Knockouts of the mouse or fruit fly gene orthologs result in lethality or severe neurological defects (Gueneau et al. 2018. PubMed ID: 29290337). BLTP1 has been cited as a non-essential gene for growth of human tissue culture cells (Online Gene Essentiality).

Clinical Sensitivity - Sequencing with CNV PGxome

The clinical sensitivity is difficult to estimate, as to date, a limited number of cases have been described in the literature. Analytical sensitivity should be high as all pathogenic variants reported to date are detectable by sequencing and NGS copy number variant analysis.

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This test provides full coverage of all coding exons of the BLTP1 gene plus 10 bases flanking noncoding DNA in all available transcripts in addition to non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

Candidates for this test are patients with clinical features of Alkuraya-Kucinskas syndrome. Targeted testing is indicated for family members of patients who have known pathogenic variants in BLTP1. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in BLTP1.


Official Gene Symbol OMIM ID
BLTP1 611565
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Alkuraya-Kucinskas syndrome AR 617822


  • Filatova et al. 2019. PubMed ID: 30485398
  • Genome Aggregation Database (gnomAD).
  • Gueneau et al. 2018. PubMed ID: 29290337
  • Guo et al. 2020. PubMed ID: 31680349
  • Kumar et al. 2020. PubMed ID: 32590954
  • Online GEne Essentiality Database (OGEE).
  • Verstreken et al. 2009. PubMed ID: 19640479


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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View Ordering Instructions

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2) Select Additional Test Options

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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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