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Congenital Limb Malformation Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
5065 ARHGAP31 81479,81479 Order Options and Pricing
B3GLCT 81479,81479
BMP2 81479,81479
BMPR1B 81479,81479
BRIP1 81479,81479
CC2D2A 81479,81479
CDH3 81479,81479
CEP290 81408,81479
CHSY1 81479,81479
COL2A1 81479,81479
DHODH 81479,81479
DOCK6 81479,81479
DYM 81479,81479
ERCC4 81479,81479
ESCO2 81479,81479
FANCA 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
FBLN1 81479,81479
FBXW4 81479,81479
FGF10 81479,81479
FGFR2 81479,81479
FGFR3 81479,81479
FIG4 81406,81479
FLNA 81479,81479
FMN1 81479,81479
GDF5 81479,81479
GLI3 81479,81479
GNAS 81479,81479
GREM1 81479,81479
HDAC4 81479,81479
HOXD13 81479,81479
IHH 81479,81479
KDM6A 81479,81479
KIF7 81479,81479
KMT2D 81479,81479
LMBR1 81479,81479
LRP4 81479,81479
MGP 81479,81479
MKS1 81479,81479
MYCN 81479,81479
NIPBL 81479,81479
NOG 81479,81479
NOTCH1 81407,81479
NSDHL 81479,81479
PALB2 81307,81479
PIGV 81479,81479
PITX1 81479,81479
RAD51C 81479,81479
RBM8A 81479,81479
RECQL4 81479,81479
ROR2 81479,81479
RPGRIP1L 81479,81479
RSPO2 81479,81479
SALL1 81479,81479
SALL4 81479,81479
SF3B4 81479,81479
SHH 81479,81479
SLX4 81479,81479
SOX9 81479,81479
TBX15 81479,81479
TBX3 81479,81479
TBX5 81405,81479
TP63 81479,81479
WNT3 81479,81479
WNT7A 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
5065Genes x (72)81479 81307(x1), 81405(x1), 81406(x1), 81407(x1), 81408(x1), 81479(x139) $1030 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 backbone).

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

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


  • Juan Dong, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Congenital limb malformation refers to both gross reduction defects and more subtle alterations in the number, length, and anatomy of the legs, arms, and digits. The prevalence is ~ 1 in 500 to 1 in 1,000 live births (Wilkie. 2003. PubMed ID: 12587917). Congenital limb malformation includes many conditions such as: preaxial/postaxial polydactyly of the foot/hand (Burger et al. 2017. PubMed ID: 28946786), brachydactyly, and limb hypoplasia-reduction (Bonafe et al. 2015. PubMed ID: 26394607).


This panel includes 72 genes associated with a variety of genetic congenital limb malformations (Wilkie. 2003. PubMed ID: 12587917; Bonafe et al. 2015. PubMed ID: 26394607). Genetic limb malformations are genetically heterogenous and can be inherited in an autosomal dominant (AD), autosomal recessive (AR), and X-linked (XL) manner.

This panel offers testing for the following and many other conditions: Brachydactyly, Ectrodactyly, Polydactyly, Syndactyly, Symphalangism, Townes-Brocks branchiootorenal-like syndrome, Duane-radial ray syndrome, Fanconi anemia, Pallister-Hall syndrome, Split-hand/foot malformation, some subtypes of Meckel syndrome, Holt-Oram syndrome, Robinow syndrome, Liebenberg syndrome, TP63-related conditions, Liebenberg syndrome, Keutel Syndrome, Smith McCort Dysplasia, Yunis-Varon Syndrome, Camptomelic Dysplasia, and Feingold syndrome 1.

See individual gene test descriptions for information on molecular biology of gene products, and spectra of pathogenic variants.

Clinical Sensitivity - Sequencing with CNV PGxome

In one study, pathogenic variants were found in 18% (36/199) of patients with a genetic etiology of Congenital Upper Limb Anomalies. Among them, 13/199 cases had a copy number variation on the chromosomal level, and 23/199 cases were found to have a pathogenic variant involving a single nucleotide substitution, or small deletion/insertion (Carli et al. 2013. PubMed ID: 24343878).

Testing Strategy

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

This panel typically provides 99.5% 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).

Some genes have multiple copies in the haploid genome. In these cases, we may only analyze a portion of these genes.

Other genes without full coverage include, but may not be limited to: CEP290, CHSY1, DOCK6, FMN1, LRP4, NIPBL, NOTCH1, FANCD2, SALL1, SALL4, SHH, SF3B4, FBXW4, SHH, SOX9, RPGRIP1L, and RBM8A. A full list of regions not covered by NGS or Sanger sequencing is available upon request.

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

Patients with limb defects should be considered.


Name Inheritance OMIM ID
Acrocallosal Syndrome, Schinzel Type AR 200990
Acrofacial Dysostosis 1, Nager Type AD 154400
Adams-Oliver Syndrome 1 AD 100300
Adams-Oliver Syndrome 2 AR 614219
Adams-Oliver Syndrome 5 AD 616028
Apert Syndrome AD 101200
Aplasia Of Lacrimal And Salivary Glands AD 180920
Brachydactyly Type A1 AD 112500
Brachydactyly Type A2 AD 112600
Brachydactyly Type C AD 113100
Brachydactyly, Type B2 AD 611377
Camptomelic Dysplasia AD 114290
Child Syndrome XL 308050
Cornelia de Lange syndrome 1 AD 122470
Cousin Syndrome AR 260660
Crouzon Syndrome AD 123500
Duane-Radial Ray Syndrome AD 607323
Ectodermal Dysplasia, Ectrodactyly, and Macular Dystrophy AR 225280
Ectrodactyly, Ectodermal Dysplasia, And Cleft Lip/Palate Syndrome 3 AD 604292
Fanconi Anemia, Complementation Group A AR 227650
Fanconi Anemia, Complementation Group C AR 227645
Fanconi Anemia, Complementation Group D2 AR 227646
Fanconi Anemia, Complementation Group E AR 600901
Fanconi Anemia, Complementation Group F AR 603467
Fanconi Anemia, Complementation Group G AR 614082
Fanconi Anemia, Complementation Group I AR 609053
Fanconi Anemia, Complementation Group J AR 609054
Fanconi Anemia, Complementation Group L AR 614083
Fanconi Anemia, Complementation Group N AR 610832
Fanconi Anemia, Complementation Group O AR 613390
Fanconi Anemia, Complementation Group P AR 613951
Fanconi anemia, Complementation Group Q AR 615272
Feingold Syndrome 1 AD 164280
Holt-Oram Syndrome AD 142900
Humerofemoral hypoplasia with radiotibial ray deficiency AR 618022
Hyperphosphatasia With Mental Retardation AR 239300
Joubert Syndrome 7 AR 611560
Joubert Syndrome 9 AR 612285
Kabuki Syndrome 1 AD 147920
Kabuki Syndrome 2 XL 300867
Keutel Syndrome AR 245150
Kniest Dysplasia AD 156550
Lacrimoauriculodentodigital Syndrome AD 149730
Liebenberg Syndrome AD 186550
Meckel Syndrome 1 AR 249000
Meckel Syndrome 4 AR 611134
Miller Syndrome AR 263750
Oto-Palato-Digital Syndrome Type 1 XL 311300
Pallister-Hall Syndrome AD 146510
Peters Plus Syndrome AR 261540
Polydactyly, Preaxial II AD 174500
Progressive Osseous Heteroplasia AD 166350
Roberts Syndrome AR 268300
Robinow Syndrome, Autosomal Recessive AR 268310
Rothmund-Thomson Syndrome AR 268400
Saethre-Chotzen Syndrome AD 101400
Single Upper Central Incisor AD 147250
Smith McCort Dysplasia AR 607326
Syndactyly Cenani Lenz Type AR 212780
Synpolydactyly 1 AD 186000
Synpolydactyly 2 AD 608180
Temtamy Preaxial Brachydactyly Syndrome AR 605282
Tetraamelia syndrome 2 AR 618021
Tetraamelia, Autosomal Recessive AR 273395
Thrombocytopenia-Absent Radius Syndrome AR 274000
Townes-Brocks Syndrome AD 107480
Ulna And Fibula Absence Of With Severe Limb Deficiency AR 276820
Ulnar-Mammary Syndrome AD 181450
Yunis-Varon Syndrome AR 216340

Related Test




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

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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1) Select Test Method (Backbone)

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2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

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