FeedbackMassively Parallel Sequencing
For tests to consider before ordering genetic testing, see Related Tests.
Massively Parallel Sequencing
- Testing for a known familial sequence variant by sequencing gene of interest. A copy of the family member’s test result documenting the familial gene variant is REQUIRED.
- To determine if the variant(s) of interest are detectable by this assay, contact an ARUP genetic counselor at 800-242-2787.
Disorders of cobalamin (vitamin B12)/propionate/homocysteine metabolism result from defects in the vitamin B12 metabolic pathway. Abnormal biochemical findings may include elevated propionylcarnitine levels and/or propionyl/acetylcarnitine ratio in plasma and increased methylmalonic acid in blood; vitamin B12 levels may be normal or elevated. The clinical features of these disorders are highly variable, with multiple systems affected, and age of disease onset ranges from the perinatal period to adulthood. Molecular testing is used to confirm suspected cobalamin/propionate/homocysteine metabolism-related disorders in individuals with clinical symptoms and/or biochemical findings.
Etiology
Pathogenic germline variants in genes associated with the cobalamin metabolic pathway cause disorders of cobalamin (vitamin B12)/propionate/homocysteine metabolism.
Prevalence
The table below details the prevalence of several disorders of cobalamin metabolism. The true prevalence of the disorders of cobalamin metabolism is unknown.
| Disorder | Prevalence |
|---|---|
|
Isolated methylmalonic acidemia |
1/50,000-100,000 |
|
Methylmalonic aciduria and homocystinuria, cblC type |
1/200,000 (overall) |
|
Homocystinuria due to cystathionine beta-synthase deficiency |
1/200,000 to 1/344,000 (worldwide) |
|
Propionic acidemia |
1/105,000-130,00 (in the U.S.) |
|
Other disorders included in this panel |
Rare |
Inheritance
Autosomal recessive for all genes tested, except for HCFC1 (X-linked) and MAT1A (autosomal dominant or autosomal recessive)
Test Interpretation
Methodology
This test is performed using the following sequence of steps:
- Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
- Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as next generation sequencing [NGS]) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline. The pipeline includes an algorithm for the detection of large (single exon-level or larger) deletions and duplications.
- Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
- Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.
Clinical Sensitivity
Variable, dependent on condition
Analytical Sensitivity
For massively parallel sequencing:
| Variant Class | Analytical Sensitivity (PPA) Estimatea (%) and 95% Credibility Region (%) |
Analytical Specificity (NPA) (%) |
|---|---|---|
|
SNVs |
>99 (96.9-99.4) |
>99.9 |
|
Deletions 1-10 bpb |
93.8 (84.3-98.2) |
>99.9 |
|
Insertions 1-10 bpb |
94.8 (86.8-98.5) |
>99.9 |
|
Exon-levelc deletions |
97.8 (90.3-99.8) [2 exons or larger] 62.5 (38.3-82.6) [single exon] |
>99.9 |
|
Exon-levelc duplications |
83.3 (56.4-96.4) [3 exons or larger] |
>99.9 |
|
aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived. These values do not apply to testing performed by multiplex ligation-dependent probe amplification (MLPA). bVariants greater than 10 bp may be detected, but the analytical sensitivity may be reduced. cIn most cases, a single exon deletion or duplication is less than 450 bp and 3 exons span a genomic region larger than 700 bp. bp, base pairs; NPA, negative percent agreement; PPA, positive percent agreement; SNVs, single nucleotide variants |
||
Limitations
- A negative result does not exclude a heritable form of cobalamin metabolism disorders.
- Diagnostic errors can occur due to rare sequence variations.
- Interpretation of this test result may be impacted if the individual has had an allogeneic stem cell transplantation.
- The following regions are not sequenced due to technical limitations of the assay:
- ABCD4 (NM_001353592, NM_001353599, NM_001353600, NM_001353609) partial exon(s) 17 (Chr14:74753377-74753383)
- ABCD4 (NM_001353594, NM_001353601, NM_001353606, NM_001353608) partial exon(s) 16 (Chr14:74753377-74753383)
- ABCD4 (NM_001353607) partial exon(s) 15(Chr14:74753377-74753383)
- ABCD4 (NM_001353610) partial exon(s) 14(Chr14:74755363-74755398)
- ABCD4 (NM_020325) partial exon(s) 18(Chr14:74753377-74753383)
- CBS (NM_001321072) exon(s) 1
- IVD (NM_001354597) exon(s) 1
- IVD (NM_001354598, NM_001354600) exon(s) 12,13
- IVD (NM_001354601) exon(s) 12
- IVD (NM_001354599, NM_001354600) partial exon(s) 2(Chr15:40699947-40700010)
- PCCA (NM_001352609) exon(s) 22
- SUCLA2 (NM_003850) partial exon(s) 8(Chr13:48528275-48528320)
- The following will not be evaluated:
- Variants outside the coding regions and intron-exon boundaries of the targeted genes
- Regulatory region variants and deep intronic variants
- Breakpoints of large deletions/duplications
- Deletions/duplications in the ADK, AHCY, and GNMT genes
- The following may not be detected:
- Deletions/duplications/insertions of any size by massively parallel sequencing
- Large duplications less than 3 exons in size
- Noncoding transcripts
- Some variants due to technical limitations in the presence of pseudogenes, repetitive, or homologous regions
- Low-level somatic variants
- Single exon deletions/duplications in the following exons:
- AMN (NM_030943) 10; CBS (NM_001321072) 1; IVD (NM_001354597) 1; IVD (NM_001354598, NM_001354600) 12-13; IVD (NM_001354601) 12; PCCA (NM_001352609) 22
Genes Tested
| Gene | MIM Number | Disorder | Inheritance |
|---|---|---|---|
|
ABCD4 |
603214 |
Methylmalonic aciduria and homocystinuria, cblJ type |
AR |
|
ACSF3 |
614245 |
Combined malonic and methylmalonic aciduria |
AR |
|
ADK |
102750 |
Hypermethioninemia due to adenosine kinase deficiency |
AR |
|
AHCY |
180960 |
Hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase |
AR |
|
AMN |
605799 |
Imerslund-Grasbeck syndrome 2 |
AR |
|
CBLIF |
609342 |
Intrinsic factor deficiency |
AR |
|
CBS |
613381 |
Homocystinuria, B6-responsive and nonresponsive types Thrombosis, hyperhomocysteinemia |
AR |
|
CD320 |
606475 |
Methylmalonic aciduria, transient, due to transcobalamin receptor defect |
AR |
| CTH | 607657 | Cystathioninuria | AR |
|
CUBN |
602997 |
Imerslund-Grasbeck syndrome 1 Proteinuria, chronic benign |
AR |
|
HCFC1 |
300019 |
Methylmalonic acidemia and homocysteinemia, cblX type; intellectual disability, X-linked 3 |
XL |
| IVD | 607036 | Isovaleric acidemia | AR |
|
LMBRD1 |
612625 |
Methylmalonic aciduria and homocystinuria, cblF type |
AR |
|
MAT1A |
610550 |
Hypermethioninemia, persistent, autosomal dominant, due to methionine adenosyltransferase I/III deficiency Methionine adenosyltransferase deficiency, autosomal recessive |
AD/AR |
|
MCEE |
608419 |
Methylmalonyl-CoA epimerase deficiency |
AR |
| MLYCD | 606761 | Malonyl-CoA decarboxylase deficiency | AR |
|
MMAA |
607481 |
Methylmalonic aciduria, vitamin B12 responsive, cblA type |
AR |
|
MMAB |
607568 |
Methylmalonic aciduria, vitamin B12 responsive, cblB type |
AR |
|
MMACHC |
609831 |
Methylmalonic aciduria and homocystinuria, cblC type |
AR |
|
MMADHC |
611935 |
Mmethylmalonic aciduria and homocystinuria, cblD type |
AR |
|
MMUT |
609058 |
Methylmalonic aciduria, mut (0) type |
AR |
|
MTHFR |
607093 |
Homocystinuria due to deficiency of (5,10)-methylenetetrahydrofolate |
AR |
|
MTR |
156570 |
Homocystinuria-megaloblastic anemia, cblG complementation type |
AR |
|
MTRR |
602568 |
Homocystinuria-megaloblastic anemia, cblE complementation type |
AR |
|
PCCA |
232000 |
Propionic acidemia |
AR |
|
PCCB |
232050 |
Propionic acidemia |
AR |
|
SUCLA2 |
603921 |
Mitochondrial DNA depletion syndrome 5 (encephalomyopathic with or without methylmalonic aciduria) |
AR |
|
SUCLG1 |
611224 |
Mitochondrial DNA depletion syndrome 9 (encephalomyopathic type with methylmalonic aciduria) |
AR |
|
TCN2 |
613441 |
Transcobalamin II deficiency |
AR |
| AD, autosomal dominant; AR, autosomal recessive; XL, X-linked | |||
25205257
Baumgartner MR, Hörster F, Dionisi-Vici C, et al. Proposed guidelines for the diagnosis and management of methylmalonic and propionic acidemia. Orphanet J Rare Dis. 2014;9:130.
Cobalamin C disease identified by newborn screening
Cusmano-Ozog K, Levine S, Martin M, et al. Cobalamin C disease identified by newborn screening: the California experience. In: Program and abstracts for the SIMD annual meeting. Mol Genet Metab. 2007:227-65. [ Accessed: Apr 2022]
GeneReviews - Isolated Methylmalonic Acidemia
Manoli I, Sloan JL, Venditti CP. Isolated methylmalonic acidemia. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Last Revision: Dec 2016; Accessed: Apr 2022]
Methylmalonic acidemia without homocystinuria
Rosenblatt D, Watkins D. Methylmalonic acidemia without homocystinuria. Orphanet. [Last update: Mar 2012; Accessed: Apr 2022]
GeneReviews - Homocystinuria Caused by Cystathionine Beta-Synthase Deficiency
Sacharow SJ, Picker JD, Levy HL. Homocystinuria caused by cystathionine beta-synthase deficiency. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-202s. [Last Update: May 2017; Accessed: Apr 2022]
19819175
Skovby F, Gaustadnes M, Mudd SH. A revisit to the natural history of homocystinuria due to cystathionine beta-synthase deficiency. Mol Genet Metab. 2010;99(1):1-3.
GeneReviews - Disorders of Intracellular Cobalamin Metabolism
Sloan JL, Carrillo N, Adams D, et al. Disorders of intracellular cobalamin metabolism. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Last Update: Dec 2021; Accessed: Apr 2022]
21841779
Sloan JL, Johnston JJ, Manoli I, et al. Exome sequencing identifies ACSF3 as a cause of combined malonic and methylmalonic aciduria. Nat Genet. 2011;43(9):883-6.
19836982
Weisfeld-Adams JD, Morrissey MA, Kirmse BM, et al. Newborn screening and early biochemical follow-up in combined methylmalonic aciduria and homocystinuria, cblC type, and utility of methionine as a secondary screening analyte. Mol Genet Metab. 2010;99(2):116-123.
Confirm suspected cobalamin (vitamin B12)/propionate/homocysteine metabolism-related disorder in individuals with clinical symptoms and/or biochemical findings. Should not be ordered to assess vitamin B12 level.