MMADHC

protein-coding

metabolism 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]

Previous symbols:
  • C2orf25

MANE transcript

NM_015702.3

Inheritance

AR

ClinVar variants

P:71U:90B:109

Top phenotype

Methylmalonic aciduria and homocystinuria, cblD type; Methylmalonic aciduria, cblD type

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr2:149,569,637-149,587,778

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~18.1 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

inborn disorder of cobalamin metabolism and transportDEFINITIVE

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.

inborn disorder of cobalamin metabolism and transportSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0019220

Submitter: PanelApp Australia

methylmalonic aciduria and homocystinuria type cblDSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010185

Submitter: Orphanet

methylmalonic aciduria and homocystinuria type cblDDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010185

Submitter: Natera

methylmalonic aciduria and homocystinuria type cblDDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010185

Submitter: G2P

inborn disorder of cobalamin metabolism and transportDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019220

Submitter: Ambry Genetics

methylmalonic aciduria and homocystinuria type cblDMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0010185

Submitter: Ambry Genetics

methylmalonic aciduria and homocystinuria type cblDSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010185

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Methylmalonic aciduria and homocystinuria, cblD type; Methylmalonic aciduria, cblD typeAR

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

Refs: 5524089; 2339678; 15292234; 18385497; 20301409; 20301503; 22156578; 35337626Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MMADHC variants in ClinVar

12 Conditions Cataloged
Methylmalonic aciduria and homocystinuria type cblDTotal: 333
not providedTotal: 41
Inborn genetic diseasesTotal: 28
Disorders of Intracellular Cobalamin MetabolismTotal: 22
not specifiedTotal: 16
MMADHC-related disorderTotal: 9
Cobalamin C diseaseTotal: 6
Isolated methylmalonic aciduria cblD typeTotal: 6

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
99
clinvar
1
clinvar
103
missense
1
clinvar
3
clinvar
78
clinvar
9
clinvar
91
nonsense
10
clinvar
10
clinvar
2
clinvar
22
start loss
1
clinvar
1
frameshift
17
clinvar
15
clinvar
2
clinvar
34
splice donor/acceptor (+/-2bp)
15
clinvar
4
clinvar
19
Total2843901081270

Highest pathogenic variant AF is 0.000037798654

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_015702.3RefSeqNP_056517.17MANE Select
ENST00000303319.10EnsemblENSP00000301920.57MANE Select
ENST00000422782.2EnsemblENSP00000408331.28Standard
ENST00000422782.3EnsemblENSP00000408331.28Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.4131681541.090.000007131934
Missense (PolyPhen)5049.7851.0043600
Synonymous-0.2465451.71.040.00000237565
Loss of Function1.581017.10.5860.00000102187

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish00.0absent
East Asian0.000270.00027rare
Finnish00.0absent
European (Non-Finnish)0.000120.00012rare
South Asian0.0000330.000033rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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