# NM_004531.5(MOCS2):c.6G>A (p.Ser2=)

https://sugi.bio/variant/mocs2-p-ser2

## Summary

**MOCS2 p.Ser2= (c.6G>A)** is classified **Uncertain significance** in MOCS2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-06-25). Very rare (popmax 0.00333%, amr); Associated with sulfite oxidase deficiency due to molybdenum cofactor deficiency type B1.

**At a glance:** Uncertain significance · review: Multiple submitters · rsID rs1300378829 · 4 submitters · 1 linked condition · very rare (popmax 0.00333%, amr)

## For patients & families {#patients}

This is a change in the MOCS2 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 4 submitters, and is linked to sulfite oxidase deficiency due to molybdenum cofactor deficiency type B1.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0017387/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [MOCS2](https://sugi.bio/atlas/gene/MOCS2/) |
| Protein change (HGVS p.) | p.Ser2= |
| Coding change (HGVS c.) | c.6G>A |
| MANE Select transcript | [NM_004531](https://www.ncbi.nlm.nih.gov/nuccore/NM_004531) |
| dbSNP | [rs1300378829](https://www.ncbi.nlm.nih.gov/snp/rs1300378829/) |
| Variant type | single nucleotide variant |
| Location | chr5:53107169-53107169 (GRCh38) |
| ClinVar | [VCV1416031](https://www.ncbi.nlm.nih.gov/clinvar/variation/1416031/) |

**All HGVS expressions:** `NC_000005.10:g.53107169C>T`, `NC_000005.9:g.52402999C>T`, `NG_008435.2:g.7600G>A`, `NM_004531.5:c.6G>A`, `NM_176806.2:c.193G>A`, `NM_176806.4:c.193G>A`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 5.075, GERP 2.16, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 15.16**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.00333%** (amr) · FAF95 0.000553% · FAF99 0.000312% · 2/59,988 in the highest group · 16/1,613,890 alleles overall — very rare (popmax 0.00333%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 0.00333% | 29,994 |
| African / African-American | 0.00267% | 37,442 |
| East Asian | 0.00223% | 44,876 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,488 |
| European (non-Finnish) | 0.000847% | 117,998 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**MOCS2** population constraint: LOEUF 1.066, pLI 0.0032064, missense-Z 0.41632. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **sulfite oxidase deficiency due to molybdenum cofactor deficiency type B1** — Definitive (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 84.07, 68% of residues very-high.

**2 experimental structure(s)** (PDB): [4AP8](https://www.rcsb.org/structure/4AP8), [5MPO](https://www.rcsb.org/structure/5MPO).

## What this gene does {#gene-function}

*Describes the biological roles of MOCS2 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** MOCS2's established molecular role includes molybdopterin synthase activity.


### Pathways affected {#pathways}

MOCS2 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Molybdenum cofactor biosynthesis](https://reactome.org/content/detail/R-HSA-947581) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** molybdopterin synthase activity.

**Biological process:** Mo-molybdopterin cofactor biosynthetic process.

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2025-06-25.

**Submitter consensus:** unanimous (4/4 Uncertain significance).

**Submission history:** 4 submissions (2023–2025); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2023-02-01 |
| Fulgent Genetics, Fulgent Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2024-01-12 |
| Mayo Clinic Laboratories, Mayo Clinic | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-06-25 |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2024-02-26 |

## Associated conditions {#conditions}

[sulfite oxidase deficiency due to molybdenum cofactor deficiency type B1](https://sugi.bio/atlas/disease/sulfite-oxidase-deficiency-due-to-molybdenum-cofactor-deficiency-type-b1/).

**Reported phenotype names (ClinVar):** Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B1, not provided, Inborn genetic diseases, Molybdenum cofactor deficiency, complementation group B, MOLYBDENUM COFACTOR DEFICIENCY, TYPE B1, Molybdenum cofactor deficiency B, Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B, none provided.

## Similar variants {#similar}

Related MOCS2 variant pages (same residue, condition, or type): [MOCS2 p.Ser2Ala](/variant/mocs2-p-ser2ala), [MOCS2 p.Ser2Leu](/variant/mocs2-p-ser2leu), [MOCS2 c.377+1G>A](/variant/mocs2-c-377-plus-1g-a), [MOCS2 p.Gln30Ter](/variant/mocs2-p-gln30ter), [MOCS2 p.Glu40Ter](/variant/mocs2-p-glu40ter), [MOCS2 p.Ter189Tyr](/variant/mocs2-p-ter189tyr), [MOCS2 p.Trp38Ter](/variant/mocs2-p-trp38ter), [MOCS2 p.Tyr11Ter](/variant/mocs2-p-tyr11ter).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 1416031). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*