MMACHC

gene
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Also known as DKFZP564I122cblC

Summary

MMACHC (metabolism of cobalamin associated C, HGNC:24525) is a protein-coding gene on chromosome 1p34.1, encoding Cyanocobalamin reductase / alkylcobalamin dealkylase (Q9Y4U1). Cobalamin (vitamin B12) cytosolic chaperone that catalyzes the reductive decyanation of cyanocob(III)alamin (cyanocobalamin, CNCbl) to yield cob(II)alamin and cyanide, using FAD or FMN as cofactors and NADPH as cosubstrate.

The exact function of the protein encoded by this gene is not known, however, its C-terminal region shows similarity to TonB, a bacterial protein involved in energy transduction for cobalamin (vitamin B12) uptake. Hence, it is postulated that this protein may have a role in the binding and intracellular trafficking of cobalamin. Mutations in this gene are associated with methylmalonic aciduria and homocystinuria type cblC.

Source: NCBI Gene 25974 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): methylmalonic aciduria and homocystinuria type cblC (Definitive, ClinGen)
  • GWAS associations: 16
  • Clinical variants (ClinVar): 694 total — 58 pathogenic, 49 likely-pathogenic
  • Phenotypes (HPO): 113
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity unscored
  • MANE Select transcript: NM_015506

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24525
Approved symbolMMACHC
Namemetabolism of cobalamin associated C
Location1p34.1
Locus typegene with protein product
StatusApproved
AliasesDKFZP564I122, cblC
Ensembl geneENSG00000132763
Ensembl biotypeprotein_coding
OMIM609831
Entrez25974

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000401061, ENST00000477188, ENST00000616135, ENST00000933807

RefSeq mRNA: 2 — MANE Select: NM_015506 NM_001330540, NM_015506

CCDS: CCDS41324, CCDS81315

Canonical transcript exons

ENST00000401061 — 4 exons

ExonStartEnd
ENSE000009059994550735645507550
ENSE000011411584550821245508364
ENSE000014568714550030045500413
ENSE000015461784550879645513382

Expression profiles

Bgee: expression breadth ubiquitous, 177 present calls, max score 82.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.1811 / max 92.3771, expressed in 1712 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
268814.33381702
26870.6861391
26890.161263

Top tissues by expression

283 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right lobe of liverUBERON:000111482.39gold quality
liverUBERON:000210781.42gold quality
hindlimb stylopod muscleUBERON:000425277.73gold quality
stromal cell of endometriumCL:000225577.52gold quality
ventricular zoneUBERON:000305377.11gold quality
mucosa of transverse colonUBERON:000499177.11gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047376.80gold quality
right atrium auricular regionUBERON:000663176.46gold quality
heart left ventricleUBERON:000208475.83gold quality
cardiac ventricleUBERON:000208275.52gold quality
cardiac atriumUBERON:000208175.49gold quality
prefrontal cortexUBERON:000045175.22gold quality
heartUBERON:000094874.05gold quality
muscle of legUBERON:000138373.89gold quality
right adrenal glandUBERON:000123373.81gold quality
apex of heartUBERON:000209873.67gold quality
gastrocnemiusUBERON:000138873.25gold quality
right adrenal gland cortexUBERON:003582772.96gold quality
rectumUBERON:000105272.88gold quality
left adrenal glandUBERON:000123472.58gold quality
ganglionic eminenceUBERON:000402372.52gold quality
cortical plateUBERON:000534372.17gold quality
left adrenal gland cortexUBERON:003582571.95gold quality
colonic epitheliumUBERON:000039771.46gold quality
adrenal glandUBERON:000236971.30gold quality
islet of LangerhansUBERON:000000671.22gold quality
adrenal tissueUBERON:001830370.89gold quality
adult mammalian kidneyUBERON:000008270.87gold quality
adrenal cortexUBERON:000123570.85gold quality
muscle organUBERON:000163070.36gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-9543yes34.79
E-ANND-3yes13.26
E-CURD-10no110.67
E-ENAD-17no87.20

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): HCFC1

miRNA regulators (miRDB)

66 targeting MMACHC, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-656-3P100.0072.152788
HSA-MIR-3162-3P100.0065.37363
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-211099.9666.681930
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-3140-3P99.8868.472069
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-674599.7465.331321
HSA-MIR-7-5P99.6770.531809
HSA-MIR-6512-3P99.6566.071468
HSA-MIR-6720-5P99.6566.221459
HSA-MIR-1251-3P99.6467.211408
HSA-MIR-182799.6368.573265
HSA-MIR-1287-3P99.6366.93492
HSA-MIR-612699.6268.09996
HSA-MIR-464399.4967.631791
HSA-MIR-208A-5P99.4270.831913
HSA-MIR-208B-5P99.4270.831952
HSA-MIR-6828-5P99.3169.211433
HSA-MIR-6878-3P99.2464.23920
HSA-MIR-642A-3P99.2367.671258
HSA-MIR-642B-3P99.2367.671258
HSA-MIR-6744-3P99.2264.41972
HSA-MIR-312599.1468.492269

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity Not yet evaluated (unscored). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • One mutation, 271dupA, in MMACHC accounted for 40% of all disease alleles. (PMID:16311595)
  • Mutation analysis of the MMACHC gene showed that both patients were homozygous for 394C –> T which suggests a founder effect in Late onset cobalamin C disorder. (PMID:17431913)
  • c.271dupA (accounting for 55% of the MMACH alleles in our cohort) followed by c.394C>T (16%) and c.331C>T (9%) were the most frequent mutations. (PMID:18164228)
  • Most patients (eight of nine patients investigated) were compound heterozygotes for the 271dupA mutation and a missense mutation. (PMID:18245139)
  • MMACHC catalyzes a reductive decyanation reaction that removes the cyanide group in vitamin B(12) or cyanocobalamin (PMID:18779575)
  • A new mutation (146_154 del CCTTCCTGG) in the MMACHC gene was detected in a Chinese family with methylmalonic aciduria. (PMID:19199254)
  • Epigenetic inactivation of the MMACHC gene is responsible for methionine dependence in human melanoma cell line MeWo-LC1. (PMID:19200761)
  • MMACHC was sequenced from the DNA of 118 cblC individuals. Eleven novel mutations were identified.Genotype-phenotype correlations of common mutations were apparent. (PMID:19370762)
  • These studies suggest that the CblC protein is responsible for early processing of both CNCbl (decyanation) and alkylcobalamins (dealkylation) in mammalian cells. (PMID:19447654)
  • MMACHC with the G147D mutation is unable to bind either cyanocobalamin or hydroxocobalamin, providing a straight forward explanation for the absence of response to either vitamin form. (PMID:19700356)
  • Mutations in MMACHC are associated with altered cellular oxidative stress and apoptosis processes in the presence or absence of vitamin B(12). (PMID:19760748)
  • Diverse and clinically significant structural heart defects appear to be highly prevalent in cblC type methylmalonic aciduria and homocystinuria. (PMID:19767224)
  • Data show that the catalytic turnover numbers for the dealkylation of methylcobalamin and 5’-deoxyadenosylcobalamin by MMACHC are 11.7 +/- 0.2 and 0.174 +/- 0.006 h(-1) at 20 degrees C, respectively. (PMID:19801555)
  • MMACHC-wt and MMACHC-R161Q are both very thermolabile proteins in their apo forms, with melting temperatures (T(m)) of 39.3+/-1.0 and 37.1+/-0.7 degrees C, respectively (PMID:20219402)
  • defects occurring in the MMACHC gene are the major cause of this disease in Chinese patients with combined methylmalonic aciduria and homocystinuria (PMID:20631720)
  • MMADHC was confirmed as a binding partner for MMACHC both in vitro (SPR) and in vivo (bacterial two-hybrid system). (PMID:21071249)
  • a structural framework provides a framework for understanding catalytic function and disease mechanism for the multifunctional MMACHC complex. (PMID:22642810)
  • The function of MMADHC is exerted through its structured C-terminal domain via interactions with MMACHC. (PMID:22832074)
  • Subcellular location of MMACHC and MMADHC, two human proteins central to intracellular vitamin B(12) metabolism. (PMID:23270877)
  • data suggest that the interaction of methionine synthase with MMACHC may play a role in the regulation of the cellular processing of cobalamins that is required for cobalamin cofactor synthesis (PMID:23825108)
  • The gene responsible for cblC, named MMACHC, catalyzes the reductive decyanation of cyanocobalamin. (PMID:24577983)
  • mutation analysis of the MMACHC gene in four patients revealed novel heterozygous mutations at nucleotide 276 (c.276G > A [p.Glu926Glu] and c.276G > T [p.Glu92Asp]), which is located at the end of exon 2. (PMID:24853097)
  • HCFC1 plays a role in craniofacial development, which is in part mediated through the regulation of MMACHC expression (PMID:25281006)
  • Results propose a model whereby membrane-bound LMBD1 and ABCD4 facilitate the vectorial delivery of lysosomal vitamin B12 to cytoplasmic MMACHC. (PMID:25535791)
  • an adult patient with bull’s eye macular lesions and no clinically relevant systemic symptoms was diagnosed with cblC by genetic screening and follow-up biochemical laboratory tests. (PMID:25687216)
  • Five different known mutations in either MUT or MMACHC genes were identified in seven of the eight Chinese patients with methyl malonic acidemia. (PMID:25982642)
  • A novel mutation p.G155R of the MMACHC gene is identified in prenatal diagnosis of combined methylmalonic aciduria and homocystinuria. (PMID:26149271)
  • MMACHC mutation was found in children diagnosed with hemolytic uremic syndrome secondary to cobalamin C disorder. (PMID:26253414)
  • These results indicated that hypergonadotropic hypogonadism may be a novel clinical manifestation of cblC disease, but more reports on additional patients are needed to support this hypothesis. (PMID:26283149)
  • the MMACHC-MMADHC complex is a 1:1 heterodimer, where the interaction region overlaps with the MMACHC-Cbl binding site (PMID:26483544)
  • Sequencing of the MMACHC gene is used for confirming the diagnosis of cblC disease. MMACHC mutations were found in all the nine patients. 7 different mutations were identified, including c.609G>A, c.455_457delCCC, c.394C>T, c.445_446insA, c.658_660delAAG, c.452A>G and IVS1+1G>A. The most frequent mutation was c.609G>A (6/9). Two patients had homozygous mutations (c.445_446insA/c.445_446insA and c.609G>A/c.609G>A). (PMID:26563984)
  • Case Report: c.567dupT,p.(Ile190Tyrfs*13) MMACHC heterozygous mutation underlying methylmalonic academia in infant. (PMID:27383490)
  • These data show that the processing of cobalamin in cytoplasm occurs in a multiprotein complex composed of at least methionine synthase, methionine synthase reductase, MMACHC and MMADHC. (PMID:27771510)
  • The crystal structure of ceCblC provides insights into how architectural differences at the alpha- and beta-faces of cobalamin promote the thiol oxidase activity of ceCblC but mute it in wild-type human CblC. (PMID:28442570)
  • Partial CblC-type inherited Methylmalonic acidemia (MMACHC heterozygous mutation exonl: c. 80A >G, c. 609G >A) can onset with severe metabolic Atypical hemolytic uremic syndrome. (PMID:29068997)
  • The epimutation is present in three generations and results from PRDX1 mutations that force antisense transcription of MMACHC. (PMID:29302025)
  • THAP11F80L exhibited a strong effect on association with the MMACHC promoter and led to a decrease in MMACHC gene transcription, suggesting that the THAP11F80L mutation is directly responsible for the observed cobalamin disorder (PMID:31905202)
  • Generation of a Human iPSC line (SDQLCHi021-A) from a patient with methylmalonic acidemia cblC type carrying compound heterozygous mutations in MMAHC gene. (PMID:32058304)
  • Analysis of fibroblasts from patients with cblC and cblG genetic defects of cobalamin metabolism reveals global dysregulation of alternative splicing. (PMID:32068834)
  • The vitamin B12 processing enzyme, mmachc, is essential for zebrafish survival, growth and retinal morphology. (PMID:32186706)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriommachcENSDARG00000043877
mus_musculusMmachcENSMUSG00000028690
rattus_norvegicusMmachcENSRNOG00000017233
caenorhabditis_elegansWBGENE00022766

Protein

Protein identifiers

Cyanocobalamin reductase / alkylcobalamin dealkylaseQ9Y4U1 (reviewed: Q9Y4U1)

Alternative names: Alkylcobalamin:glutathione S-alkyltransferase, CblC, Cyanocobalamin reductase (cyanide-eliminating), Methylmalonic aciduria and homocystinuria type C protein

All UniProt accessions (2): Q9Y4U1, A0A0C4DGU2

UniProt curated annotations — full annotation on UniProt →

Function. Cobalamin (vitamin B12) cytosolic chaperone that catalyzes the reductive decyanation of cyanocob(III)alamin (cyanocobalamin, CNCbl) to yield cob(II)alamin and cyanide, using FAD or FMN as cofactors and NADPH as cosubstrate. Cyanocobalamin constitutes the inactive form of vitamin B12 introduced from the diet, and is converted into the active cofactors methylcobalamin (MeCbl) involved in methionine biosynthesis, and 5’-deoxyadenosylcobalamin (AdoCbl) involved in the TCA cycle. Forms a complex with the lysosomal transporter ABCD4 and its chaperone LMBRD1, to transport cobalamin across the lysosomal membrane into the cytosol. The processing of cobalamin in the cytosol occurs in a multiprotein complex composed of at least MMACHC, MMADHC, MTRR (methionine synthase reductase) and MTR (methionine synthase) which may contribute to shuttle safely and efficiently cobalamin towards MTR in order to produce methionine. Also acts as a glutathione transferase by catalyzing the dealkylation of the alkylcob(III)alamins MeCbl and AdoCbl, using the thiolate of glutathione for nucleophilic displacement to generate cob(I)alamin and the corresponding glutathione thioether. The conversion of incoming MeCbl or AdoCbl into a common intermediate cob(I)alamin is necessary to meet the cellular needs for both cofactors. Cysteine and homocysteine cannot substitute for glutathione in this reaction.

Subunit / interactions. Monomer in the absence of bound substrate. Homodimer; dimerization is triggered by binding to FMN or adenosylcobalamin. Interacts with LMBRD1 and ABCD4; the interaction ensures the transport of cobalamin from the lysosome to the cytoplasm. Forms a multiprotein complex with MMADHC, MTR and MTRR; the interaction with MTR could modulate MMACHC-dependent processing of cobalamin. Heterodimer with MMADHC; the interaction might play a role in the regulation of the balance between AdoCbl and MeCbl synthesis.

Subcellular location. Cytoplasm. Cytosol.

Tissue specificity. Widely expressed. Expressed at higher level in fetal liver. Also expressed in spleen, lymph node, thymus and bone marrow. Weakly or not expressed in peripheral blood leukocytes.

Disease relevance. Methylmalonic aciduria and homocystinuria, cblC type (MAHCC) [MIM:277400] An autosomal recessive disorder of cobalamin metabolism characterized by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl). Affected individuals may have developmental, hematologic, neurologic, metabolic, ophthalmologic, and dermatologic clinical findings. Although considered a disease of infancy or childhood, some individuals develop symptoms in adulthood. The disease is caused by variants affecting the gene represented in this entry.

Cofactor. Can utilize both FAD and FMN.

Similarity. Belongs to the MMACHC family.

RefSeq proteins (2): NP_001317469, NP_056321* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR032037MMACHCFamily

Pfam: PF16690

Enzyme classification (BRENDA):

  • EC 2.5.1.151 — alkylcobalamin dealkylase (BRENDA: 2 organisms, 20 substrates, 0 inhibitors, 0 Km, 12 kcat entries)

Substrate kinetics (BRENDA)

9 substrates with measured Km, best-characterized 9. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
5’-DEOXYADENOSYLCOBALAMIN0
BUTYRYLCOBALAMIN0
CYANOCOBALAMIN0
ETHYLCOBALAMIN0
HEXYLCOBALAMIN0
METHYLCOBALAMIN0
NITROCOBALAMIN0
PENTYLCOBALAMIN0
PROPYLCOBALAMIN0

Catalyzed reactions (Rhea), 4 shown:

  • 2 cob(II)alamin-[cyanocobalamin reductase] + 2 hydrogen cyanide + NADP(+) = 2 cyanocob(III)alamin + 2 apo-[cyanocobalamin reductase] + NADPH + H(+) (RHEA:16113)
  • apo-[alkylcobalamin reductase] + an R-cob(III)alamin + glutathione = cob(I)alamin-[alkylcobalamin reductase] + an S-substituted glutathione + H(+) (RHEA:40719)
  • apo-[alkylcobalamin reductase] + methylcob(III)alamin + glutathione = S-methyl glutathione + cob(I)alamin-[alkylcobalamin reductase] + H(+) (RHEA:63132)
  • apo-[alkylcobalamin reductase] + adenosylcob(III)alamin + glutathione = S-adenosylglutathione + cob(I)alamin-[alkylcobalamin reductase] + H(+) (RHEA:63136)

UniProt features (56 total): sequence variant 15, helix 15, strand 9, binding site 5, modified residue 4, mutagenesis site 3, turn 2, chain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

7 structures.

PDBMethodResolution (Å)
7WUZX-RAY DIFFRACTION1.93
3SC0X-RAY DIFFRACTION1.95
3SBZX-RAY DIFFRACTION2
3SOMX-RAY DIFFRACTION2.4
5UOSX-RAY DIFFRACTION2.51
3SBYX-RAY DIFFRACTION2.71
9MRSX-RAY DIFFRACTION3.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y4U1-F186.410.76

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (5): 104; 115–118; 129–131; 149; 160

Post-translational modifications (4): 279, 245, 247, 275

Mutagenesis-validated functional residues (3):

PositionPhenotype
122reduced affinity for cyanocobalamin.
206impairs protein folding.
230reduced activity in dealkylation of methylcobalamin.

Function

Pathways and Gene Ontology

Reactome pathways

11 pathways

IDPathway
R-HSA-3359473Defective MMADHC causes MMAHCD
R-HSA-3359474Defective MMACHC causes MAHCC
R-HSA-9759218Cobalamin (Cbl) metabolism
R-HSA-1430728Metabolism
R-HSA-1643685Disease
R-HSA-196741Cobalamin (Cbl, vitamin B12) transport and metabolism
R-HSA-196849Metabolism of water-soluble vitamins and cofactors
R-HSA-196854Metabolism of vitamins and cofactors
R-HSA-3296469Defects in cobalamin (B12) metabolism
R-HSA-3296482Defects in vitamin and cofactor metabolism
R-HSA-5668914Diseases of metabolism

MSigDB gene sets: 501 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GOBP_NEGATIVE_REGULATION_OF_NEURON_APOPTOTIC_PROCESS, GOBP_REGULATION_OF_ERBB_SIGNALING_PATHWAY, GOBP_NEGATIVE_REGULATION_OF_ERBB_SIGNALING_PATHWAY, ROVERSI_GLIOMA_COPY_NUMBER_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_MAPK_CASCADE, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_DEMETHYLATION, KEGG_ERBB_SIGNALING_PATHWAY, GOBP_COBALAMIN_METABOLIC_PROCESS, GOBP_ERBB_SIGNALING_PATHWAY, CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP

GO Biological Process (3): glutathione metabolic process (GO:0006749), cobalamin metabolic process (GO:0009235), demethylation (GO:0070988)

GO Molecular Function (10): oxidoreductase activity (GO:0016491), transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765), cobalamin binding (GO:0031419), demethylase activity (GO:0032451), cyanocobalamin reductase (cyanide-eliminating) (NADP+) activity (GO:0033787), protein homodimerization activity (GO:0042803), glutathione binding (GO:0043295), FAD binding (GO:0071949), protein binding (GO:0005515), transferase activity (GO:0016740)

GO Cellular Component (2): cytoplasm (GO:0005737), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-8 pathways:

CategoryPathways
Defects in cobalamin (B12) metabolism2
Cobalamin (Cbl, vitamin B12) transport and metabolism1
Metabolism of water-soluble vitamins and cofactors1
Metabolism of vitamins and cofactors1
Metabolism1
Defects in vitamin and cofactor metabolism1
Diseases of metabolism1
Disease1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
catalytic activity3
cellular anatomical structure2
modified amino acid metabolic process1
sulfur compound metabolic process1
tetrapyrrole metabolic process1
metabolic process1
transferase activity1
vitamin binding1
tetrapyrrole binding1
heterocyclic compound binding1
oxidoreductase activity, acting on metal ions, NAD or NADP as acceptor1
identical protein binding1
protein dimerization activity1
anion binding1
modified amino acid binding1
oligopeptide binding1
sulfur compound binding1
flavin adenine dinucleotide binding1
binding1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

1348 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MMACHCLMBRD1Q9NUN5972
MMACHCMMADHCQ9H3L0964
MMACHCMMAAQ8IVH4947
MMACHCMMABQ96EY8947
MMACHCMMUTP22033910
MMACHCMTRQ99707902
MMACHCDGKEP52429780
MMACHCMTRRQ9UBK8773
MMACHCABCD4O14678735
MMACHCCFHR5Q9BXR6633
MMACHCCFHR1Q03591616
MMACHCADAMTS13Q76LX8613
MMACHCCFHP08603606
MMACHCCD320Q9NPF0596
MMACHCMCEEQ96PE7593

IntAct

16 interactions, top by confidence:

ABTypeScore
TEPSINAP4M1psi-mi:“MI:0914”(association)0.700
Mmadhcpsi-mi:“MI:0407”(direct interaction)0.620
MMADHCpsi-mi:“MI:0407”(direct interaction)0.560
MMACHCCCT6Bpsi-mi:“MI:0915”(physical association)0.500
MTRMMACHCpsi-mi:“MI:0915”(physical association)0.470
MMACHCMTRpsi-mi:“MI:2364”(proximity)0.470
SELENBP1CAMKMTpsi-mi:“MI:0914”(association)0.350
BNIP5GNPATpsi-mi:“MI:0914”(association)0.350
SELENBP1ZNF24psi-mi:“MI:0914”(association)0.350
MMACHCTCP1psi-mi:“MI:0914”(association)0.350
SELENBP1TRMT5psi-mi:“MI:0914”(association)0.350

BioGRID (19): UBE2L3 (Co-fractionation), MMACHC (Affinity Capture-MS), MMACHC (Affinity Capture-RNA), MMACHC (Affinity Capture-MS), MMACHC (Affinity Capture-MS), TCP1 (Affinity Capture-MS), CCT2 (Affinity Capture-MS), CCT7 (Affinity Capture-MS), CCT4 (Affinity Capture-MS), MMACHC (Affinity Capture-MS), CCT6B (Affinity Capture-MS), MMACHC (Affinity Capture-MS), CCT3 (Affinity Capture-MS), PDCL (Affinity Capture-MS), CCT6A (Affinity Capture-MS)

ESM2 similar proteins: A0A0B5AC19, A1VN15, A2C538, A2CBW9, A2CCP5, A4XT72, A5GIZ3, A5GVQ6, A8IC17, A9KC01, A9NA93, O52512, O89748, P03513, P04873, P08463, P14961, P45944, P52132, P72848, P77206, P84786, Q00124, Q02189, Q02190, Q0ICV5, Q16BB4, Q1GLD5, Q1I6K3, Q3AMK3, Q3AUU4, Q3AWA8, Q46IM1, Q51320, Q5N3S5, Q5N5A3, Q6E0W8, Q6LLK0, Q7NEK3, Q7U4M7

Diamond homologs: Q5E9C8, Q5RFU5, Q5ZL21, Q7Z144, Q9CZD0, Q9Y4U1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

694 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic58
Likely pathogenic49
Uncertain significance264
Likely benign195
Benign22

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1076507NM_015506.3(MMACHC):c.449T>A (p.Ile150Lys)Pathogenic
1076669NM_015506.3(MMACHC):c.123dup (p.Pro42fs)Pathogenic
1252060NM_015506.3(MMACHC):c.352C>T (p.Gln118Ter)Pathogenic
1334896NM_015506.3(MMACHC):c.187del (p.Leu63fs)Pathogenic
1368644NM_015506.3(MMACHC):c.315C>A (p.Tyr105Ter)Pathogenic
1421NM_015506.3(MMACHC):c.271dup (p.Arg91fs)Pathogenic
1423NM_015506.3(MMACHC):c.394C>T (p.Arg132Ter)Pathogenic
1424NM_015506.3(MMACHC):c.331C>T (p.Arg111Ter)Pathogenic
1446343NM_015506.3(MMACHC):c.419G>A (p.Trp140Ter)Pathogenic
1453962NC_000001.10:g.(?45965995)(45966095_?)delPathogenic
1454386NM_015506.3(MMACHC):c.534del (p.Lys178fs)Pathogenic
1459897NC_000001.10:g.(?45974458)(45974897_?)delPathogenic
161117NM_015506.3(MMACHC):c.276G>T (p.Glu92Asp)Pathogenic
161119NM_015506.3(MMACHC):c.464G>A (p.Gly155Glu)Pathogenic
1938082NM_015506.3(MMACHC):c.151_152del (p.Leu51fs)Pathogenic
2024522NM_015506.3(MMACHC):c.81+1G>TPathogenic
2027786NM_015506.3(MMACHC):c.477_478insCATCCGAGGGGTAGTGCTGCTGCCAGGGATAGAGGTGCCAGATCTGCCACCCAGAAAACCTCATGACTGTGTACCTACAAGAGCTGAC (p.Ile160delinsHisProArgGlySerAlaAlaAlaArgAspArgGlyAlaArgSerAlaThrGlnLysThrSerTer)Pathogenic
203823NM_015506.3(MMACHC):c.3G>A (p.Met1Ile)Pathogenic
203825NM_015506.3(MMACHC):c.217C>T (p.Arg73Ter)Pathogenic
203827NM_015506.3(MMACHC):c.420G>A (p.Trp140Ter)Pathogenic
203834NM_015506.3(MMACHC):c.445_446del (p.Cys149fs)Pathogenic
203835NM_015506.3(MMACHC):c.328_331del (p.Asn110fs)Pathogenic
2068815NM_015506.3(MMACHC):c.433del (p.Ile145fs)Pathogenic
2130931NM_015506.3(MMACHC):c.81+2T>CPathogenic
2202756NM_015506.3(MMACHC):c.14_24del (p.Val5fs)Pathogenic
2504060NM_015506.3(MMACHC):c.321_329delinsACACC (p.Asn110fs)Pathogenic
2676630NM_015506.3(MMACHC):c.228_231del (p.Asp77fs)Pathogenic
2717233NM_015506.3(MMACHC):c.93C>A (p.Tyr31Ter)Pathogenic
2725295NM_015506.3(MMACHC):c.1A>T (p.Met1Leu)Pathogenic
2733897NM_015506.3(MMACHC):c.126_141del (p.Leu43fs)Pathogenic

SpliceAI

542 predictions. Top by Δscore:

VariantEffectΔscore
1:45507548:GAG:Gdonor_gain1.0000
1:45507548:GAGGT:Gdonor_loss1.0000
1:45507549:AGG:Adonor_loss1.0000
1:45507550:GGT:Gdonor_loss1.0000
1:45507552:T:Adonor_loss1.0000
1:45508202:A:AGacceptor_gain1.0000
1:45508202:ACT:Aacceptor_gain1.0000
1:45508203:C:Gacceptor_gain1.0000
1:45508204:T:Aacceptor_gain1.0000
1:45508207:TCCA:Tacceptor_loss1.0000
1:45508208:CCA:Cacceptor_loss1.0000
1:45508208:CCAG:Cacceptor_gain1.0000
1:45508209:CAG:Cacceptor_gain1.0000
1:45508210:A:AGacceptor_gain1.0000
1:45508210:AGA:Aacceptor_gain1.0000
1:45508211:G:Cacceptor_gain1.0000
1:45508211:G:GAacceptor_gain1.0000
1:45508211:GA:Gacceptor_gain1.0000
1:45508211:GAGC:Gacceptor_gain1.0000
1:45508211:GAGCC:Gacceptor_gain1.0000
1:45508363:AG:Adonor_loss1.0000
1:45508364:GGT:Gdonor_loss1.0000
1:45508366:T:Gdonor_loss1.0000
1:45511411:CACA:Cacceptor_gain1.0000
1:45511412:ACA:Aacceptor_gain1.0000
1:45511413:CA:Cacceptor_gain1.0000
1:45511413:CAC:Cacceptor_gain1.0000
1:45511414:ACT:Aacceptor_loss1.0000
1:45511415:C:CCacceptor_gain1.0000
1:45500378:C:Gdonor_gain0.9900

AlphaMissense

1806 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:45507434:A:CS54R0.995
1:45507436:C:AS54R0.995
1:45507436:C:GS54R0.995
1:45508838:T:CF158L0.993
1:45508840:T:AF158L0.993
1:45508840:T:GF158L0.993
1:45508297:C:AA121D0.992
1:45508835:T:AW157R0.991
1:45508835:T:CW157R0.991
1:45508813:C:GC149W0.990
1:45507449:T:CF59L0.989
1:45507451:T:AF59L0.989
1:45507451:T:GF59L0.989
1:45508952:T:CF196L0.987
1:45508954:C:AF196L0.987
1:45508954:C:GF196L0.987
1:45508811:T:CC149R0.985
1:45509030:T:GY222D0.984
1:45508305:G:CA124P0.982
1:45508812:G:AC149Y0.982
1:45508830:G:AG155E0.982
1:45508839:T:CF158S0.982
1:45508306:C:AA124D0.981
1:45507518:T:CC82R0.980
1:45508294:C:AA120E0.980
1:45508315:C:AA127D0.980
1:45509033:T:CF223L0.980
1:45509035:C:AF223L0.980
1:45509035:C:GF223L0.980
1:45508819:C:AH151Q0.979

dbSNP variants (sampled 300 via entrez): RS1000037450 (1:45504287 G>C), RS1000250797 (1:45507222 A>G), RS1000355237 (1:45510918 T>C), RS1000410685 (1:45510632 C>A), RS1000688178 (1:45512743 C>G,T), RS1000976572 (1:45506801 C>T), RS1001148146 (1:45500812 C>T), RS1001170788 (1:45513345 G>A), RS1001194334 (1:45512301 G>A,C), RS1001596498 (1:45500782 T>G), RS1001626236 (1:45506134 G>A), RS1001774683 (1:45511999 G>A,T), RS1001918843 (1:45513080 A>C), RS1001973766 (1:45511631 C>A), RS1002236397 (1:45507805 T>C)

Disease associations

OMIM: gene MIM:609831 | disease phenotypes: MIM:277400, MIM:251000, MIM:277410

GenCC curated gene-disease

DiseaseClassificationInheritance
methylmalonic aciduria and homocystinuria type cblCDefinitiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
methylmalonic aciduria and homocystinuria type cblCDefinitiveAR

Mondo (7): methylmalonic aciduria and homocystinuria type cblC (MONDO:0010184), atypical hemolytic-uremic syndrome (MONDO:0016244), methylmalonic aciduria and homocystinuria (MONDO:0016826), methylmalonic aciduria due to methylmalonyl-CoA mutase deficiency (MONDO:0009612), methylmalonic aciduria and homocystinuria type cblD (MONDO:0010185), homocystinuria (MONDO:0004737), inherited retinal dystrophy (MONDO:0019118)

Orphanet (7): Methylmalonic acidemia with homocystinuria (Orphanet:26), Methylmalonic acidemia with homocystinuria, type cblC (Orphanet:79282), Atypical hemolytic uremic syndrome (Orphanet:2134), Vitamin B12-unresponsive methylmalonic acidemia (Orphanet:27), Homocystinuria without methylmalonic aciduria (Orphanet:622), Methylmalonic acidemia with homocystinuria, type cblD (Orphanet:79283), OBSOLETE: Inherited retinal disorder (Orphanet:71862)

HPO phenotypes

113 total (30 of 113 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000083Renal insufficiency
HP:0000093Proteinuria
HP:0000112Nephropathy
HP:0000206Glossitis
HP:0000238Hydrocephalus
HP:0000252Microcephaly
HP:0000276Long face
HP:0000319Smooth philtrum
HP:0000348High forehead
HP:0000369Low-set ears
HP:0000400Macrotia
HP:0000505Visual impairment
HP:0000546Retinal degeneration
HP:0000580Pigmentary retinopathy
HP:0000639Nystagmus
HP:0000648Optic atrophy
HP:0000707Abnormality of the nervous system
HP:0000708Atypical behavior
HP:0000709Psychosis
HP:0000726Dementia
HP:0000751Personality changes
HP:0000790Hematuria
HP:0000952Jaundice
HP:0000980Pallor
HP:0001116Macular pseudocoloboma
HP:0001249Intellectual disability
HP:0001250Seizure
HP:0001251Ataxia
HP:0001252Hypotonia

GWAS associations

16 associations (top):

StudyTraitp-value
GCST002087_8Homocysteine levels2.000000e-09
GCST005950_15Body mass index x sex x age interaction (4df test)2.000000e-10
GCST005951_56Body mass index1.000000e-06
GCST005952_8Body mass index (age>50)9.000000e-12
GCST005954_4Body mass index x age interaction2.000000e-07
GCST006990_2Cerebrospinal AB1-42 levels in Alzheimer’s disease dementia3.000000e-07
GCST007320_18Alzheimer’s disease or family history of Alzheimer’s disease7.000000e-25
GCST007827_3Alzheimer’s disease or HDL levels (pleiotropy)1.000000e-97
GCST007827_5Alzheimer’s disease or HDL levels (pleiotropy)7.000000e-74
GCST007827_6Alzheimer’s disease or HDL levels (pleiotropy)7.000000e-54
GCST007827_7Alzheimer’s disease or HDL levels (pleiotropy)5.000000e-50
GCST007827_8Alzheimer’s disease or HDL levels (pleiotropy)3.000000e-36
GCST007848_3LDL cholesterol6.000000e-30
GCST008152_195Weight9.000000e-06
GCST009496_8Alzheimer’s disease (onset between ages 58 and 79)3.000000e-11
GCST010243_209Apolipoprotein B levels0.000000e+00

EFO canonical traits (10, from GWAS)

EFO IDTrait name
EFO:0004578homocysteine measurement
EFO:0004340body mass index
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0004670beta-amyloid 1-42 measurement
EFO:0009268family history of Alzheimer’s disease
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004338body weight
EFO:0004615apolipoprotein B measurement

MeSH disease descriptors (6)

DescriptorNameTree numbers
D065766Atypical Hemolytic Uremic SyndromeC12.050.351.968.419.936.463.500; C12.200.777.419.936.463.500; C12.950.419.936.463.500; C15.378.050.141.610.500; C15.378.140.855.925.500.500; C15.378.243.937.925.500.500
D006712HomocystinuriaC10.228.140.163.100.365; C16.320.565.100.480.500; C16.320.565.189.365; C17.300.428; C18.452.132.100.365; C18.452.648.100.480.500; C18.452.648.189.365
D058499Retinal DystrophiesC11.768.585.658
C564743Methylmalonic Aciduria and Homocystinuria, CblD Type (supp.)
C565390Methylmalonic Aciduria due to Methylmalonyl-CoA Mutase Deficiency (supp.)
C537359Methylmalonic acidemia with homocystinuria (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

41 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases abundance, increases expression3
(+)-JQ1 compounddecreases expression3
Acetaminophendecreases expression2
Tobacco Smoke Pollutiondecreases expression2
Cyclosporinedecreases expression2
Aflatoxin B1decreases expression, decreases methylation2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
aminomethylphosphonic acid (AMPA)decreases expression1
dicrotophosincreases expression1
pirinixic acidincreases expression, affects binding, increases activity1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
isobutyl alcoholaffects cotreatment, decreases expression, increases abundance1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
cylindrospermopsinincreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic aciddecreases expression1
abrinedecreases expression1
NSC 689534affects binding, decreases expression1
Sunitinibdecreases expression1
Air Pollutantsaffects expression, increases abundance1
Arsenicincreases abundance, increases expression1
Benzo(a)pyrenedecreases expression1
Copperaffects binding, decreases expression1
Doxorubicindecreases expression1
Ethyl Methanesulfonatedecreases expression1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Hydroxocobalaminaffects binding1

Cellosaurus cell lines

57 cell lines: 51 finite cell line, 4 cancer cell line, 2 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B3WEWG1070Finite cell line
CVCL_B3WFWG1127Finite cell line
CVCL_B3WGWG1129Finite cell line
CVCL_B3WHWG1135Finite cell line
CVCL_B3WIWG1391Finite cell line
CVCL_B3WJWG1404Finite cell line
CVCL_B3WKWG1481Finite cell line
CVCL_B3WLWG1496Finite cell line
CVCL_B3WQWG1692Finite cell line
CVCL_B3WRWG2339Finite cell line

Clinical trials (associated diseases)

95 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT02574403PHASE4COMPLETEDStudy Assessing an Algorithm-based Strategy of Eculizumab Discontinuation in Children and Adults With aHUS
NCT07308574PHASE4RECRUITINGPost-Marketing Clinical Study of Ravulizumab in Participants With Clinical aHUS
NCT02949128PHASE3COMPLETEDStudy of ALXN1210 in Complement Inhibitor Treatment-Naïve Adult and Adolescent Participants With Atypical Hemolytic Uremic Syndrome (aHUS)
NCT03131219PHASE3COMPLETEDStudy of Ravulizumab in Children and Adolescents With Atypical Hemolytic Uremic Syndrome (aHUS)
NCT03205995PHASE3TERMINATEDSafety and Efficacy Study of OMS721 in Patients With Atypical Hemolytic Uremic Syndrome
NCT04861259PHASE3ACTIVE_NOT_RECRUITINGA Study Evaluating the Efficacy, Safety, Pharmacokinetics and Pharmacodynamics of Crovalimab in Adult and Adolescent Participants With Atypical Hemolytic Uremic Syndrome (aHUS)
NCT04889430PHASE3COMPLETEDEfficacy and Safety of Iptacopan (LNP023) in Adult Patients With Atypical Hemolytic Uremic Syndrome Naive to Complement Inhibitor Therapy
NCT04958265PHASE3ACTIVE_NOT_RECRUITINGA Study Evaluating the Efficacy, Safety, Pharmacokinetics and Pharmacodynamics of Crovalimab in Pediatric Participants With Atypical Hemolytic Uremic Syndrome (aHUS)
NCT05795140PHASE3RECRUITINGEvaluate Long-term Safety, Tolerability and Efficacy of Iptacopan in Study Participants With aHUS
NCT05935215PHASE3RECRUITINGEfficacy and Safety of Switching From Anti-C5 Antibody Treatment to Iptacopan Treatment in Study Participants With Atypical Hemolytic Uremic Syndrome (aHUS)
NCT06247085PHASE3RECRUITINGA Study to Investigate Efficacy and Safety of Pegtibatinase Compared With Placebo in Participants ≥12 to ≤65 Years of Age With Classical Homocystinuria (HCU) Due to Cystathionine Beta Synthase Deficiency Receiving Standard of Care Treatment
NCT06431893PHASE3ENROLLING_BY_INVITATIONA Long-term Extension Study to Assess the Long-term Safety and Efficacy of Pegtibatinase Treatment in Participants ≥5 to ≤65 Years of Age With Classical Homocystinuria (HCU) (ENSEMBLE)
NCT04224207PHASE3COMPLETEDManagement of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT07082855PHASE3NOT_YET_RECRUITINGA Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT00838513PHASE2COMPLETEDOpen Label Controlled Trial of Eculizumab in Adult Patients With Plasma Therapy-sensitive Atypical Hemolytic Uremic Syndrome (aHUS)
NCT00844428PHASE2COMPLETEDOpen Label Controlled Trial of Eculizumab in Adolescent Patients With Plasma Therapy-Sensitive aHUS
NCT00844545PHASE2COMPLETEDOpen Label Controlled Trial of Eculizumab in Adult Patients With Plasma Therapy-Resistant aHUS
NCT00844844PHASE2COMPLETEDOpen Label Controlled Trial of Eculizumab in Adolescent Patients With Plasma Therapy-Resistant aHUS
NCT01193348PHASE2COMPLETEDAn Open-Label, Multi-Center Clinical Trial of Eculizumab in Pediatric Patients With Atypical Hemolytic-Uremic Syndrome
NCT01194973PHASE2COMPLETEDAn Open-label, Multi-center Clinical Trial of Eculizumab in Adult Patients With Atypical Hemolytic-uremic Syndrome
NCT01757431PHASE2COMPLETEDThe Safety and Efficacy of Eculizumab in Japanese Patients With Atypical Hemolytic Uremic Syndrome (aHUS)
NCT02464891PHASE2TERMINATEDComplement Inhibition in aHUS Dialysis Patients
NCT03303313PHASE2WITHDRAWNA Study of an Investigational Drug, Cemdisiran (ALN-CC5), in Patients With Atypical Hemolytic Uremic Syndrome
NCT03518203PHASE2COMPLETEDEculizumab to Treat Thrombotic Microangiopathy/Atypical Hemolytic Uremic Syndrome -Associated Multiple Organ Dysfunction Syndrome in Hematopoietic Stem Cell Transplant Recipients
NCT03999840PHASE2WITHDRAWNEculizumab to Cemdisiran Switch in aHUS
NCT04725812PHASE2TERMINATEDComplement Regulation to Undo Systemic Harm in Preeclampsia
NCT00483314PHASE2COMPLETEDHomocystinuria: Treatment With N-Acetylcysteine
NCT02404337PHASE2COMPLETEDBetaine METABOLISM OF PATIENTS With Homocystinuria
NCT03763227PHASE2COMPLETEDIntravitreal Ranibizumab (Lucentis®) in the Treatment of Non-leaking Macular Cysts in Retinal Dystrophy
NCT04068207PHASE2COMPLETEDMinocycline Treatment in Retinitis Pigmentosa
NCT04945772PHASE2COMPLETEDEfficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT05462132PHASE1COMPLETEDSafety, Tolerability and Pharmacodynamics of SYNB1353 in Healthy Adult Volunteers
NCT05902962PHASE1COMPLETEDSAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects
NCT06319872PHASE1RECRUITINGThe Effects of Disulfiram (Antabuse®) on Visual Acuity in Patients With Retinal Degeneration
NCT06455826PHASE1COMPLETEDMAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects (Wallaby)
NCT03655223Not specifiedENROLLING_BY_INVITATIONEarly Check: Expanded Screening in Newborns
NCT01522170Not specifiedTERMINATEDaHUS Observational Long Term Follow-Up
NCT01522183Not specifiedRECRUITINGAtypical Hemolytic-Uremic Syndrome (aHUS) Registry
NCT01755429Not specifiedCOMPLETEDTo Characterize the Safety and Tolerability of Eculizumab in Two Japanese aHUS Patients
NCT01770951Not specifiedCOMPLETEDA Retrospective, Observational, Non-interventional Trial to Assess Eculizumab Treatment Effect in Patients With Atypical Hemolytic Uremic Syndrome (aHUS)