MOCS2 p.Ser2=
c.6G>A · rs1300378829 · VCV1416031
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
Conditions
1
sulfite oxidase deficiency due to molybdenum cofactor deficiency type B1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.098 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 15.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/59,988 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000312%
Overall
0.000991%
16/1,613,890 alleles · very rare
exomes 13/1,461,822 · genomes 3/152,068 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 29,994 |
| African / African-American | 0.00267% | 37,442 |
| East Asian | 0.00223% | 44,876 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| European (non-Finnish) | 0.000847% | 117,998 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- MOCS2
- Protein
- p.Ser2=
- Coding
- c.6G>A
- MANE Select
- NM_004531
- dbSNP
- rs1300378829
- Type
- single nucleotide variant
- Location
- chr5:53107169 (GRCh38)
- Gene constraint
- LOEUF 1.066 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.07 · 2 PDB
Similar variants
- MOCS2 p.Ser2Ala Uncertain significance ★ ⚠ same residue
- MOCS2 p.Ser2Leu Likely benign ★ same residue
- MOCS2 c.377+1G>A Pathogenic/Likely pathogenic ★★ same condition
- MOCS2 p.Gln30Ter Pathogenic/Likely pathogenic ★★ same condition
- MOCS2 p.Glu40Ter Pathogenic/Likely pathogenic ★★ same condition
- MOCS2 p.Ter189Tyr Pathogenic/Likely pathogenic ★★ same condition
- MOCS2 p.Trp38Ter Likely pathogenic ★★ same condition
- MOCS2 p.Tyr11Ter Pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/mocs2-p-ser2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown