MOCS3

protein-coding

molybdenum cofactor synthesis 3, the group of Ubiquitin like modifier activating enzymes

Gene summary

Molybdenum cofactor (MoCo) is necessary for the function of all molybdoenzymes. The protein encoded by this gene adenylates and activates molybdopterin synthase, an enzyme required for biosynthesis of MoCo. This gene contains no introns. A pseudogene of this gene is present on chromosome 14. [provided by RefSeq, Nov 2012]

MANE transcript

NM_014484.5

Inheritance

AR

ClinVar variants

U:231B:81

Top phenotype

MOCS3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr20:50,958,818-50,963,929

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~5.1 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

sulfite oxidase deficiency due to molybdenum cofactor deficiencyMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0020480

Submitter: PanelApp Australia

sulfite oxidase deficiency due to molybdenum cofactor deficiency type B2LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0980701

Submitter: ClinGen

*MOCS3 *was first reported in relation to “sulfite oxidase deficiency due to molybdenum cofactor deficiency type B2”, an autosomal recessive disorder of molybdenum cofactor (moco) biosynthesis, in 2017 (Huijmans et al, PMID: 28544736). This is the only known disease entity asserted to be caused by variants in *MOCS3*. Moco deficiency has been shown to be caused by variants in genes involved in moco biosynthesis, including *MOCS1*, *MOCS2*, and *GEPH*. There is a spectrum of clinical severity. The most severe cases present shortly after birth with neonatal-onset severe encephalopathy, refractory seizures, opisthotonos, hypotonia, feeding difficulties, and apnea. Brain MRI changes MRI changes like hypoxic–ischemic lesions. Most patients die in infancy. Individuals with milder, late-onset condition often present with acute neurologic decompensation during illness, with altered mental state, dystonia, choreoathetosis, ataxia, nystagmus, and fluctuating hypotonia and hypertonia (Misko et al, 2021, PMID: 34870926; Johannes et al, 2022, PMID: 36296488). The clinical features are believed to be related to loss of sulfite oxidase (SOX) activity, one of four human proteins that require moco to function. Reduction of SOX activity results in accumulation of sulfite and secondary metabolites, S-sulfocysteine and thiosulfate, that are toxic, as well as a decrease in cysteine and cystine. Three variants (two missense, one nonsense) that have been reported in 2 probands in 2 publications were scored in this curation. The first reported patient was noted to have a mild phenotype with normal or low normal uric acid levels in plasma and urine, normal urine sulfite level, and normal sulfite oxidase activity, unlike patients with severe moco deficiency (Huijmans et al, 2017, PMID: 28544736). The second patient reported had a severe neonatal onset; sulfite oxidase activity was not reported (Tian et al, 2021, PMID: 33897766). In addition to these two cases, molecular analysis of a pregnancy loss with non-immune hydrops fetalis identified homozygosity for a nonsense variant (Shamseldin et al, 2018, PMID: 28749478; SCV001870500.1). A subsequent report indicated that the variant had been found in homozygosity in an individual with “no phenotype”; details of the age of the homozygous individual and evaluation were not provided (Aladbi et al, 2025, PMID: 3950496). This gene-disease relationship supported by experimental evidence including the biochemical function of the gene product and its interaction with MOCS2A, one of the two proteins encoded by *MOCS2*, a gene previously classified as having a definitive relationship with “sulfite oxidase deficiency due to molybdenum cofactor deficiency type B1”. MOCS3 activates MOCS2A by ATP-dependent adenylation and formation of a thiocarboxylate group, required for molybdopterin (MPT) synthesis (Matthies et al, 2004, PMID: 15073332; Chowdhury, 2012, PMID: 22453920; Johannes et al, 2022, PMID: 36296488). In summary, there is limited evidence supporting the relationship between *MOCS3* and autosomal recessive “sulfite oxidase deficiency due to molybdenum cofactor deficiency type B2”. This classification was approved by the ClinGen General Inborn Errors of Metabolism Gene Curation Expert Panel on April 24, 2026 (SOP v12).

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MOCS3 variants in ClinVar

6 Conditions Cataloged
not providedTotal: 283
not specifiedTotal: 58
MOCS3-related disorderTotal: 5
EBV-positive nodal T- and NK-cell lymphomaTotal: 2
Non-immune hydrops fetalisTotal: 1
Combined molybdoflavoprotein enzyme deficiencyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014484.5. 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
18
clinvar
67
clinvar
4
clinvar
89
missense
192
clinvar
7
clinvar
3
clinvar
202
nonsense
9
clinvar
9
start loss
3
clinvar
3
frameshift
9
clinvar
9
splice donor/acceptor (+/-2bp)
0
Total00231747312
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_014484.5RefSeqNP_055299.11MANE Select
ENST00000244051.3EnsemblENSP00000244051.11MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Sulfur relay system - Homo sapiens (human)
  • Metabolism
  • Molybdenum cofactor biosynthesis
  • Metabolism of water-soluble vitamins and cofactors
  • Metabolism of vitamins and cofactors

Biological Process

  • tRNA wobble uridine modification
  • tRNA wobble position uridine thiolation
  • Mo-molybdopterin cofactor biosynthetic process
  • enzyme active site formation via cysteine modification to L-cysteine persulfide
  • molybdopterin cofactor biosynthetic process

Molecular Function

  • thiosulfate sulfurtransferase activity
  • protein binding
  • ATP binding
  • nucleotidyltransferase activity
  • sulfurtransferase activity

Cellular Component

  • cytoplasm
  • cytosol

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000244051
Coding exons
1
Length
2458
Individuals with no LoFs
0
Homozygous LoFs
0
Heterozygous LoFs
0
Defined
0
p
0.00
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.6712462770.8870.00001542880
Missense (PolyPhen)6381.3430.77449880
Synonymous0.007061291290.9990.000006811072
Loss of Function0.6441012.50.8036.76e-7136

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of cytosolic tRNA(Lys), tRNA(Glu) and tRNA(Gln). Also essential during biosynthesis of the molybdenum cofactor. Acts by mediating the C-terminal thiocarboxylation of sulfur carriers URM1 and MOCS2A. Its N-terminus first activates URM1 and MOCS2A as acyl-adenylates (-COAMP), then the persulfide sulfur on the catalytic cysteine is transferred to URM1 and MOCS2A to form thiocarboxylation (-COSH) of their C-terminus. The reaction probably involves hydrogen sulfide that is generated from the persulfide intermediate and that acts as nucleophile towards URM1 and MOCS2A. Subsequently, a transient disulfide bond is formed. Does not use thiosulfate as sulfur donor; NFS1 probably acting as a sulfur donor for thiocarboxylation reactions. {ECO:0000255|HAMAP-Rule:MF_03049, ECO:0000269|PubMed:15073332, ECO:0000269|PubMed:19017811}.;

Recessive Scores

pRec
0.196

Intolerance Scores

LoFtool
0.641
RVIS EVS
-0.36
RVIS percentile EVS
29.16

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.918

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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