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VACTERL Association and Related Disorders Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
ARID5A 81479,81479
AXIN1 81479,81479
B9D1 81479,81479
BAZ1A 81479,81479
BMP2 81479,81479
BRCA1 and BRCA2 81162
BRIP1 81479,81479
CC2D2A 81479,81479
CHD7 81407,81479
COX4I1 81479,81479
DACT1 81479,81479
DSTYK 81479,81479
DYNC2H1 81479,81479
EFTUD2 81479,81479
EP300 81479,81479
ERCC4 81479,81479
ETV3L 81479,81479
FANCA 81479,81479
FANCB 81479,81479
FANCC 81479,81479
FANCD2 81479,81479
FANCE 81479,81479
FANCF 81479,81479
FANCG 81479,81479
FANCI 81479,81479
FANCL 81479,81479
FANCM 81479,81479
FGF8 81479,81479
FOXF1 81479,81479
FOXG1 81404,81479
FREM2 81479,81479
GLI3 81479,81479
HAAO 81479,81479
HOXD13 81479,81479
IFT172 81479,81479
JAG1 81407,81406
KDM6A 81479,81479
KMT2A 81479,81479
KMT2D 81479,81479
KYNU 81479,81479
LMO7 81479,81479
LPP 81479,81479
MAD2L2 81479,81479
MID1 81479,81479
MIR17HG 81479,81479
MKKS 81479,81479
MNX1 81479,81479
MYCN 81479,81479
NADSYN1 81479,81479
NCAPD3 81479,81479
NOTCH2 81479,81479
OTX2 81479,81479
PALB2 81307,81479
PCSK5 81479,81479
PIGN 81479,81479
PTCH1 81479,81479
PTEN 81321,81323
PUF60 81479,81479
RAD51 81479,81479
RAD51C 81479,81479
RBM8A 81479,81479
RECQL4 81479,81479
RERE 81479,81479
RFWD3 81479,81479
RFX6 81479,81479
SALL1 81479,81479
SALL4 81479,81479
SEMA3E 81479,81479
SHH 81479,81479
SLX4 81479,81479
SPECC1L 81479,81479
SUFU 81479,81479
TBX1 81479,81479
TBX5 81405,81479
TCOF1 81479,81479
TRAP1 81479,81479
TWIST1 81404,81403
UBE2T 81479,81479
WDR26 81479,81479
WDR35 81479,81479
XRCC2 81479,81479
ZIC3 81479,81479
ZNF17 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
13041Genes x (84)81479 81162(x1), 81307(x1), 81321(x1), 81323(x1), 81403(x1), 81404(x2), 81405(x1), 81406(x1), 81407(x2), 81479(x154) $1190 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our Custom Panel tool.

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


  • Erin Sybouts, PhD

Clinical Features and Genetics

Clinical Features

VACTERL association (also known as VATER association) is the nonrandom occurrence of three or more of the following birth defects: vertebral defects, anal atresia, cardiac defects, tracheal-esophageal fistula, renal anomalies, and limb abnormalities. In addition to these major clinical features, VACTERL patients may less commonly have additional phenotypes including, but not limited to, genitourinary anomalies, single umbilical artery, strabismus, cloaca, and duodenal atresia (Solomon et al. 2010. PubMed ID: 20683998). Although there are many phenotypes of VACTERL that overlap with those of other congenital disorders, individuals with VACTERL do not have ophthalmologic anomalies, brain malformations, or hearing loss (Solomon. 2011. PubMed ID: 21846383); presence of any of these phenotypes may be indicative of an alternative condition.

The estimated incidence of VACTERL ranges from 1 in 10,000 to 1 in 40,000 infants, depending on the diagnostic criteria used (Solomon. 2018. PubMed ID: 30580478).

Disorders that share notable phenotype overlap with VACTERL association include Alagille syndrome, CHARGE syndrome, Currarino syndrome, Fanconi anemia, Feingold syndrome, VACTERL with hydrocephalus, Baller-Gerold syndrome, Holt-Oram syndrome, Opitz G/BBB syndrome, Pallister-Hall syndrome, Townes-Brocks syndrome, basal cell nevus syndrome, McKusick-Kaufman syndrome, TAR (thrombocytopenia with absent radius) syndrome, Fryns syndrome, MURCS (Müllerian duct aplasia, unilateral renal aplasia, and cervicothoracic somite dysplasia) association, hemifacial microsomia, and 22q11.2 deletion syndrome.

This test will not genetically confirm a VACTERL diagnosis. Rather, this test is intended to rule out potential alternative causes of the phenotypes observed in a patient suspected to have VACTERL. As many of the disorders that have phenotype overlap with VACTERL have known genetic components, genetic testing is crucial to establish a diagnosis per exclusionem (by exclusion). It has been recommended that a genetics-first approach is used for patients suspected of VACTERL to prevent misdiagnosis (van de Putte et al. 2020. PubMed ID: 32656166). Other advantages of testing may include reproductive planning and prenatal testing to follow up ultrasound results. 


VACTERL is an association of congenital malformations that occur together in a nonrandom fashion. However, the basis of each of these anomalies in an individual may not arise from a single cause, implying the inherent heterogeneity of this condition (Solomon. 2018. PubMed ID: 30580478). As such, limited information on genetic causes of VACTERL is currently available, though a small number of candidate genes with potential disease-causing variants have been identified in a restricted number of VACTERL cases.

This test includes candidate genes that have been associated with VACTERL association as well as genes that have been shown to be causative of other disorders that show significant phenotypic overlap. The genes on this panel have diverse functions; however, many of them have critical roles in development such as tissue-specific gene expression, modification of epigenetic marks, DNA repair, or regulation of cell growth. The genes on this panel also vary in their modes of inheritance. As a general trend, causative variants in many genes on this panel that cause autosomal dominant disorders often arise de novo

Copy number variants at various regions throughout the genome have been suggested to be causative of VACTERL association. Recurrent CNVs associated with VACTERL include 1p35.3 deletion, 8q24.3 duplication, 10q25.3 duplication, 17q23.3 deletion, 22q11.2 duplication, and Xp22.3 duplication (Brosens et al. 2013. PubMed ID: 23653573).

See individual gene summaries for more information about molecular biology of gene products and spectra of pathogenic variants.

Clinical Sensitivity - Sequencing with CNV PGxome

As VACTERL association is heterogeneous and is diagnosed based on exclusion of phenotypically similar disorders, it is difficult to estimate the clinical sensitivity of this specific grouping of genes. In terms of the related syndromes, the clinical sensitivity (if known) varies, as shown in the summary table below.

Syndrome Gene(s) Clinical Sensitivity References
Alagille Syndrome JAG1, NOTCH2 ~97% Spinner et al. 1993. PubMed ID: 20301450
Baller-Gerold Syndrome RECQL4 >95% Van Maldergem et al. 1993. PubMed ID: 20301383
Basal Cell Nevus Syndrome PTCH1, SUFU >60% Evans et al. 2002. PubMed ID: 20301330
CAKUT DSTYK ~2% Sanna-Cherchi et al. 2013. PubMed ID: 23862974
CHARGE Syndrome CHD7 65-70% Lalani et al. 1993. PubMed ID: 20301296
Currarino Syndrome MNX1 ~50% Crétolle et al. 2008. PubMed ID: 18449898
Fanconi Anemia  BRCA2, BRIP1, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, ERCC4, FANCL, FANCM, MAD2L2, PALB2, RAD51, RAD51C, RFWD3, SLX4, UBE2T, XRCC2 >90% Mehta et al. 1993. PubMed ID: 20301575
Feingold Syndrome MYCN, MIR17HG >60% Marcelis et al. 1993. PubMed ID: 20301770
Holt-Oram Syndrome TBX5 >70% McDermott et al. 2004. PubMed ID: 20301290
Joubert Syndrome CC2D2A ~50% Valente et al. 2013. PubMed ID: 23403901
McKusick-Kaufman Syndrome MKKS ~100% Slavotinek. 2002. PubMed ID: 20301675
Opitz G/BBB Syndrome MID1 ~25% Meroni. 2004. PubMed ID: 20301502
Pallister-Hall Syndrome GLI3 >90% Biesecker. 2000. PubMed ID: 20301638
Short Rib Thoracic Dysplasia with/without Polydactyly DYNC2H1, IFT172 ~33% Schmidts et al. 2013. PubMed ID: 23456818
TAR Syndrome RBM8A ~95% Toriello. 2009. PubMed ID: 20301781
Townes-Brocks Syndrome SALL1, DACT1 ~75% Kohlhase. 2007. PubMed ID: 20301618
22q11.2 Deletion Syndrome Gross Deletion at 22q11.2 (via CMA) 100% McDonald-McGinn et al. 1999. PubMed ID: 20301696

Testing Strategy

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

This panel typically provides 99.0% average coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define 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).

Exons 4-5 of RERE, exons 1-4 of NOTCH2, and exon 1 of MNX1 are not covered in this test due to high paralogy.

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 testing include individuals with multiple VACTERL phenotypes (vertebral defects, anal atresia, cardiac defects, tracheal-esophageal fistula, renal anomalies, or limb abnormalities) observed prenatally via ultrasound or in neonates through various modalities. 


Name Inheritance OMIM ID
Alagille Syndrome 1 AD 118450
Alagille Syndrome 2 AD 610205
Alveolar Capillary Dysplasia With Misalignment Of Pulmonary Veins AD 265380
Aml - Acute Myeloid Leukemia 601626
Baller-Gerold Syndrome AR 218600
Bardet-Biedl Syndrome 6 AR 605231
Brachydactyly Type A2 AD 112600
Brachydactyly, Type D AD 113200
Brachydactyly, Type E1 AD 113300
Brachydactyly-Syndactyly Syndrome 610713
Caudal Duplication Anomaly 607864
CHARGE Association AD 214800
COACH syndrome 2 619111
Congenital Anomalies of Kidney and Urinary Tract, Susceptibility to AD 610805
Conotruncal Heart Malformations 217095
Cowden Disease AD 158350
Cranioectodermal Dysplasia 2 AR 613610
Craniosynostosis, Type 1 AD 123100
Cryptophthalmos, unilateral or bilateral, isolated AR 123570
Currarino Syndrome AD 176450
Deafness, congenital heart defects, and posterior embryotoxon 617992
Digeorge Sequence AD 188400
Duane-Radial Ray Syndrome AD 607323
Fallot Tetralogy AD 187500
Familial Colorectal Cancer 114500
Fanconi Anemia, Complementation Group A AR 227650
Fanconi Anemia, Complementation Group B XL 300514
Fanconi Anemia, Complementation Group C AR 227645
Fanconi Anemia, Complementation Group D1 AR 605724
Fanconi Anemia, Complementation Group D2 AR 227646
Fanconi Anemia, Complementation Group E AR 600901
Fanconi Anemia, Complementation Group F 603467
Fanconi Anemia, Complementation Group G 614082
Fanconi Anemia, Complementation Group I AR 609053
Fanconi Anemia, Complementation Group J 609054
Fanconi Anemia, Complementation Group L AR 614083
Fanconi Anemia, Complementation Group N 610832
Fanconi Anemia, Complementation Group O AR 613390
Fanconi Anemia, Complementation Group P AR 613951
Fanconi anemia, Complementation Group Q AR 615272
Fanconi Anemia, Complementation Group R AD 617244
Fanconi Anemia, Complementation Group S AR 617883
Fanconi Anemia, Complementation Group T AR 616435
Fanconi Anemia, Complementation Group U AR 617247
Fanconi Anemia, Complementation Group V AR 617243
Fanconi Anemia, Complementation Group W AR 617784
Feingold Syndrome 1 AD 164280
Feingold Syndrome 2 AD 614326
Fraser Syndrome 2 AR 617666
Gorlin Syndrome AD 109400
Greig Cephalopolysyndactyly Syndrome AD 175700
Hajdu-Cheney Syndrome AD 102500
Heterotaxy, Visceral, X-Linked XL 306955
Holoprosencephaly 3 AD 142945
Holoprosencephaly 7 AD 610828
Holt-Oram Syndrome AD 142900
Hydroxykynureninuria AR 236800
Hypertelorism, Teebi type AD 145420
Ivic Syndrome AD 147750
Joubert Syndrome 27 AR 617120
Joubert Syndrome 32 AR 617757
Joubert Syndrome 9 AR 612285
Kabuki Syndrome 1 AD 147920
Kabuki Syndrome 2 XL 300867
Kallmann Syndrome 5 AD 612370
Kallmann Syndrome 6 AD 612702
Macrocephaly/Autism Syndrome AD 605309
Mandibulofacial dysostosis, Guion-Almeida type AD 610536
Mckusick Kaufman Syndrome AR 236700
Meckel Syndrome 6 AR 612284
Meckel Syndrome 9 AR 614209
Menke-Hennekam syndrome 2 AD 618333
Microcephaly 22, primary, autosomal recessive AR 617984
Microphthalmia Syndromic 5 AD 610125
Microphthalmia, Isolated, With Coloboma 5 AD 611638
Mirror movements 2 AD 614508
Mitchell-Riley syndrome AR 615710
Mitochondrial complex IV deficiency, nuclear type 16 AR 619060
Multiple Congenital Anomalies-Hypotonia-Seizures Syndrome AR 614080
Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart AD 616975
Oculomaxillofacial Dysostosis AD 600251
Opitz G/BBB Syndrome, Type I XL 300000
Opitz GBBB syndrome, type II AD 145410
Pallister-Hall Syndrome AD 146510
Pituitary Hormone Deficiency, Combined, 6 AD 613986
Polydactyly Preaxial Type 4 AD 174700
Polydactyly, Postaxial, Type A1 AD 174200
Premature ovarian failure 15 AR 618096
Premature ovarian failure 17 619146
Rapadilino Syndrome AR 266280
Retinitis Pigmentosa 71 AR 616394
Rett Syndrome, Congenital Variant AD 613454
Robinow-Sorauf Syndrome AD 180750
Rothmund-Thomson Syndrome AR 268400
Rubinstein-Taybi Syndrome 2 AD 613684
Saethre-Chotzen Syndrome AD 101400
Schizencephaly 269160
Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies AD 617877
Short-Rib Thoracic Dysplasia 10 with or without Polydactyly AR 615630
Short-Rib Thoracic Dysplasia 3 with or without Polydactyly AR 613091
Short-Rib Thoracic Dysplasia 7 with or without Polydactyly AR 614091
Single Upper Central Incisor AD 147250
Skraban-Deardorff syndrome AD 617616
Spastic Paraplegia 23 AR 270750
Spermatogenic failure 619145
Spermatogenic failure 28 AR 618086
Sweeney-Cox syndrome AD 617746
Syndactyly Type 5 AD 186300
Synpolydactyly 1 AD 186000
Thrombocytopenia-Absent Radius Syndrome AR 274000
Townes-Brocks Syndrome AD 107480
Townes-Brocks syndrome 2 AD 617466
Treacher Collins Syndrome AD 154500
VACTERL Association With Hydrocephaly, X-Linked XL 314390
Velocardiofacial Syndrome AD 192430
Verheij syndrome AD 615583
Vertebral, cardiac, renal, and limb defects syndrome 1 AR 617660
Vertebral, cardiac, renal, and limb defects syndrome 2 AR 617661
Vertebral, cardiac, renal, and limb defects syndrome 3 AR 618845
Wiedemann-Steiner Syndrome AD 605130
Wilms' Tumor 194070
Xeroderma Pigmentosum, Complementation Group F AR 278760
XFE Progeroid Syndrome AR 610965

Related Tests

Alagille Syndrome Panel
CHARGE and Kallmann Syndromes Panel
Congenital Abnormalities of the Kidney and Urinary Tract (CAKUT) Panel
Congenital Limb Malformation Panel
PGmaxTM - Comprehensive Congenital Heart Disease Panel



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.
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  • 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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