MMADHC
protein-codingmetabolism of cobalamin associated D
Gene summary
This gene encodes a mitochondrial protein that is involved in an early step of vitamin B12 metabolism. Vitamin B12 (cobalamin) is essential for normal development and survival in humans. Mutations in this gene cause methylmalonic aciduria and homocystinuria type cblD (MMADHC), a disorder of cobalamin metabolism that is characterized by decreased levels of the coenzymes adenosylcobalamin and methylcobalamin. Pseudogenes have been identified on chromosomes 11 and X.[provided by RefSeq, Nov 2008]
- C2orf25
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0019220
Submitter: ClinGen
The relationship between MMADHC and autosomal recessive “inborn disorder of cobalamin metabolism and transport” was evaluated using the ClinGen Clinical Validity Framework as of April 13, 2021. MMADHC is involved in the intracellular conversion of cobalamin to its two coenzymes, adenosylcobalamin (AdoCbl) in mitochondria and methylcobalamin (MeCbl) in the cytoplasm, where it is involved in the metabolism of methylmalonic acid and homocysteine respectively. Dependent upon the type and location of the variant(s) within MMADHC, patients have either methylmalonic aciduria (MMA), homocystinuria (HC), or both (combined phenotype). For the purposes of this curation, these biochemical phenotypes were lumped together under an inborn disorder of cobalamin metabolism and transport. Of note, MMADHC has been reported to result in the cblD complementation group of cobalamin disorders. Biallelic variants in MMADHC were first reported in patients with cblD cobalamin disorder in 2008 (Coelho et al, 2008 PMID 18385497). Data from 11 probands who are homozygous or compound heterozygous for MMADHC variants were curated, including 14 unique variants (missense, inframe duplication, frameshift, nonsense, intronic) from three publications (Coelho et al, 2008, PMID 18385497; Miousse et al, 2009, PMID 19058814; Wang et al, 2018, PMID 30334532). More data is available in the literature but the maximum points for genetic evidence (12 points) has been reached. The gene-disease relationship is supported by the biochemical function of MMADHC, which is consistent with the biochemical features in patients with MMADHC variants (Gherasim et al, 2013, PMID 23415655; Jusufi et al, 2014, PMID 24722857), interaction of the MMADHC gene product with that of MMACHC which also causes an inborn disorder of cobalamin metabolism and transport resulting in homocystinuria and methylmalonic aciduria (Plesa et al, 2011, PMID 21071249; Froese et al, 2015, PMID 26483544), functional alterations studies in which variants from patients with cblD disorder were expressed in cblD fibroblasts showing that the type and location of the variants correlates with the biochemical phenotype (Stucki et al, 2012, PMID 22156578) and rescue studies with wild type MMADHC (Coelho et al, PMID 18385497). In summary, MMADHC is definitively associated with an inborn disorder of cobalamin metabolism and transport. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This clinical validity classification was approved by the ClinGen Aminoacidopathy Gene Curation Expert Panel on April 30, 2021.
Inheritance Pattern: AR
Disease ID:MONDO:0019220
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0010185
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0010185
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:0010185
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0019220
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0010185
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0010185
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Hematologic; Neurologic; Ophthalmologic
Intervention: Biochemical
Rationale: In Homocystinuria-megaloblastic anemia, cblD type, medical management (eg, with betaine, folic acid, and OH-cobalamin) has been described as beneficial; In Methylmalonic aciduria, cblD type, B12 therapy has been reported as beneficial
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MMADHC variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015702.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 99 | 1 | 103 | ||
| missense | 1 | 3 | 78 | 9 | 91 | |
| nonsense | 10 | 10 | 2 | 22 | ||
| start loss | 1 | 1 | ||||
| frameshift | 17 | 15 | 2 | 34 | ||
| splice donor/acceptor (+/-2bp) | 15 | 4 | 19 | |||
| Total | 28 | 43 | 90 | 108 | 1 | 270 |
Highest pathogenic variant AF is 0.000037798654
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056517.1 | 7 | MANE Select | |
| Ensembl | ENSP00000301920.5 | 7 | MANE Select | |
| Ensembl | ENSP00000408331.2 | 8 | Standard | |
| Ensembl | ENSP00000408331.2 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cobalamin (Cbl, vitamin B12) transport and metabolism
- Metabolism
- Metabolism of water-soluble vitamins and cofactors
- Metabolism of vitamins and cofactors
Biological Process
- coenzyme biosynthetic process
- cobalamin metabolic process
Molecular Function
- protein binding
Cellular Component
- cytoplasm
- mitochondrion
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000428879
- Coding exons
- 7
- Length
- 18183
- Individuals with no LoFs
- 125716
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 24
- Defined
- 125740
- p
- 0.0000954
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.413 | 168 | 154 | 1.09 | 0.00000713 | 1934 |
| Missense (PolyPhen) | 50 | 49.785 | 1.0043 | 600 | ||
| Synonymous | -0.246 | 54 | 51.7 | 1.04 | 0.00000237 | 565 |
| Loss of Function | 1.58 | 10 | 17.1 | 0.586 | 0.00000102 | 187 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00012 | 0.00012 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in cobalamin metabolism (PubMed:18385497, PubMed:23415655, PubMed:24722857, PubMed:26364851). Plays a role in regulating the biosynthesis of two coenzymes, methylcobalamin and adenosylcobalamin (PubMed:18385497, PubMed:24722857). Plays a role in regulating the proportion of methylcobalamin and adenosylcobalamin (PubMed:23415655, PubMed:24722857). Promotes oxidation of cob(II)alamin bound to MMACHC (PubMed:26364851). {ECO:0000269|PubMed:18385497, ECO:0000269|PubMed:23415655, ECO:0000269|PubMed:24722857, ECO:0000269|PubMed:26364851}.;
Recessive Scores
- pRec
- 0.133
Intolerance Scores
- LoFtool
- 0.313
- RVIS EVS
- 0.48
- RVIS percentile EVS
- 79.25
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.531
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |