A new test for all MODY genes

New DNA sequencing technology allows us to test for pathogenic variants in all the genes known to cause diabetes diagnosed outside of the neonatal period in a single test rather than analysing just one or two genes at a time. This targeted next generation sequencing test simultaneously analyses 54 genes and 19 mtDNA loci in which pathogenic variants have been reported to cause MODY or diabetes as part of a monogenic syndrome such as MIDD (maternally inherited diabetes and deafness) or RCAD (renal cysts and diabetes syndrome). Testing for pathogenic variants in multiple genes increases the number of patients in whom a monogenic form of diabetes is identified and identifies patients with syndromic subtypes of monogenic diabetes where there is no clinical suspicion of the disorder (Colclough et al 2022 Diabetes 71: 530-537, PMID: 34789499 http://link.springer.com/article/10.1007%2Fs00125-013-2962-5).

Which genes/Genetic subtypes are included in the test?

*Genes*	*Phenotype*
GCK	Persistent and mild fasting hyperglycaemia from birth
HNF1A and HNF4A	Common forms of MODY that can be treated with sulphonylureas
KCNJ11 and ABCC8	Rare forms of MODY that can be treated with sulphonylureas
HNF1B	Renal/urogenital structural abnormalities and diabetes
CEL	Diabetes and exocrine dysfunction
NEUROD1, INS, PDX1, RFX6 and APPL1	Rare, non-syndromic, autosomal dominant forms of MODY
PCBD1, PLAGL1 and ZFP57	Rare, non-syndromic, autosomal recessive forms of MODY
AKT2, CAV1, CIDEC, LIPE, LMNA, PLIN1 and PPARG	Partial lipodystrophy, dyslipidaemia and insulin resistance
AGPAT2, BSCL2 and CAVIN1	Congenital generalised lipodystrophy
INSR	Severe insulin resistance without lipodystrophy and dyslipidaemia
PCNT	Severe insulin resistance and microcephalic osteodysplastic primordial dwarfism type II (MOPD2)
WRN	Severe insulin resistance, progeria and cataracts
FBN1, KCNJ6, MFN2, MTX2, OTULIN, POLD1, PSMB8, ZMPSTE24	Lipodystrophy as part of a monogenic syndrome
PAX6	Diabetes and aniridia
MAFA	Diabetes and insulinomatosis
MANF	Diabetes, hypothyroidism, hypogonadism, short stature, ID, obesity, deafness, high myopia, microcephaly and alopecia
DUT	Diabetes and bone marrow failure
GATA4 and GATA6	Diabetes and cardiac malformations
WFS1 and CISD2	Wolfram syndrome (diabetes, optic atrophy and deafness)
PPP1R15B, TRMT10A and DUT	Autosomal recessive juvenile-onset diabetes with microcephaly
DCAF17	Woodhouse Sakati syndrome (alopecia, hypogonadism, hearing impairment, diabetes, learning disabilities and extrapyramidal manifestations)
ZBTB20	Primrose syndrome (tall stature, macrocephaly, intellectual disability, disturbed behaviour, unusual facial features, diabetes, deafness, progressive muscle wasting and ectopic calcifications)
DNAJC3	Autosomal recessive juvenile-onset diabetes with central and peripheral neurodegeneration
DYRK1B	Diabetes and metabolic syndrome
PIK3R1 and PRKCE	Diabetes and SHORT syndrome (short stature, hyperextensibility, hernia, ocular depression, Rieger anomaly, and teething delay)
SLC29A3	H syndrome (hyperpigmentation, hypertrichosis, hepatosplenomegaly, heart anomalies, hearing loss, hypogonadism, low height, and hyperglycaemia) and PHID syndrome (pigmented hypertrichosis with insulin dependent diabetes)
Mitochondrial DNA variants m.3243A>G, m.3761C>A, m.4289T>C, m.7471dup, m.7512T>C, m.8344A>G, m.8356T>C, m.8561C>G, m.8993T>C, m.9155A>G, m.9267G>C, m.11778G>A, m.12168G>A, m.12258C>A, m.12271T>C, m.12317T>C, m.13051G>A, m.14483A>G and m.14709T>C	Mitochondrial diabetes

When should I request this test and how much does it cost?

The cost of this test is centrally funded by NHS England for NHSE patients meeting eligibility criteria (see Guidelines for Genetic Testing in MODY // Diabetes Genes). This test for 54 monogenic diabetes genes costs £650 for NHS referrals outside of England and £813 (£650 plus a 25% surcharge) for non-NHS referrals. An online probability calculator can predict the likelihood of MODY according to a patient’s clinical characteristics. Please contact the Exeter team for advice regarding the appropriateness of the referral and the best testing strategy for your patient (kevin.colclough@nhs.net or 01392 408324).

What sample is required?

What is the reporting time for this test?

Can the test identify a pathogenic variant that is known to cause a disease other than diabetes?

Potentially, yes. The test includes the LMNA gene in which pathogenic variants cause a range of phenotypes including partial lipodystrophy, Emery-Dreifuss muscular dystrophy, Charcot-Marie-Tooth disease type 2B, limb girdle muscular dystrophy type 1b, Hutchinson-Gifford Progeria syndrome and dilated cardiomyopathy. More than 200 patients with partial lipodystrophy have been tested in our laboratory and no pathogenic variants causing other phenotypes have been identified. Therefore the likelihood of finding a pathogenic variant that predisposes to, for example, dilated cardiomyopathy is low. For patients with a clinical suspicion of a monogenic form of lipodystrophy, we sequence a panel of genes that includes FBN1. Pathogenic variants in this gene cause Marfan syndrome (MFS) but a subset of variants occurring within the penultimate exon 64 result in a recently recognised syndrome consisting of partial manifestations of Marfan syndrome, a progeroid facial appearance, and clinical features of lipodystrophy (Passarge et al 2016 PMID: 26860060, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989216/). Analysis of the FBN1 gene will be limited to detecting only known pathogenic variants in exon 64 causing Marfanoid–progeroid–lipodystrophy syndrome to avoid identifying a variant associated with classic MFS.

The test includes genes such as WFS1, HNF1B, GATA6 and the mitochondrial DNA variant m.3243A>G where diabetes occurs as part of a syndromic disorder. The clinical expressivity and penetrance of the extra-pancreatic features are highly variable in these syndromes, and diabetes can be the only presenting feature at the time of testing for monogenic diabetes. This test can therefore potentially result in an unexpected diagnosis of a syndromic disorder (Colclough et al 2022 PMID: 34789499). In these scenarios we will contact the referring clinician to discuss the clinical significance of this result for the patient and their family, and whether referral to a clinical genetics service is required, prior to issuing the formal report.

The test includes the ABCC8 and KCNJ11 genes since pathogenic activating variants cause sulphonylurea responsive diabetes. Congenital hyperinsulinism results from recessive inactivating ABCC8 and KCNJ11 variants; carrier status for hyperinsulinism (identification of a heterozygous inactivating variant) will not be reported.

The test also includes a number of genes that cause recessively inherited forms of monogenic diabetes. It is therefore possible that heterozygous carriers of pathogenic variants in these genes will be identified. These heterozygous variants will not be disease-causing in these individuals and their carrier status will not be reported.

What are the test limitations?

This test will identify the same types of pathogenic variants detected by Sanger sequencing as well as large deletions or duplications previously identified by a separate dosage assay. The test sensitivity is estimated at >97.5% (95% CI). Balanced translocations, inversions and intronic variants located outside of the conserved splice site sequences will not be detected. There are some parts of the human genome that are not amenable to next generation sequencing, including a small part of the GATA6 gene. Pathogenic variants in GATA6 cause pancreatic agenesis with cardiac and other anomalies, but a few patients diagnosed with diabetes in adolescence/adulthood have been reported (De Franco et al 2012 Diabetes 62: 993-997) so this region will be analysed by Sanger sequencing for patients with a cardiac abnormality.

Sequencing a greater number of genes will identify more novel/rare variants whose clinical significance is uncertain. These include variants not seen before or identified in a small number of patients where the causal link to the disease is unproven. The clinical report will only include likely pathogenic variants or variants of uncertain significance where further investigation is recommended (for example by testing diabetic relatives to see if they have the same possible mutation). New clinical or genetic information may change the interpretation of pathogenicity. In accordance with best practice guidelines, known benign variants of no clinical significance are not reported.

Where can I find more technical information about the test?

Genetic Test Referral Forms