Cobalamin/Propionate/Homocysteine Metabolism-Related Disorders Panel

Content Review: May 2022 Last Update:
  • Use to confirm suspected cobalamin (vitamin B12)/propionate/homocysteine metabolism-related disorder in individuals with clinical symptoms and/or biochemical findings
  • Do not use to assess vitamin B12 concentrations
  • If a familial sequence variant has been previously identified, targeted sequencing for that variant may be appropriate; refer to the Laboratory Test Directory for additional information

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.

Genetics

Genes

See Genes Tested table for genes included in the panel.

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

Analytic Sensitivity

For MPS:

Variant Class Analytic Sensitivity (PPA) Estimatea (%)
and 95% Credibility Region (%)		 Analytic 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 analytic 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 MPS
    • 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