MOCS2 p.Ser9=
c.27G>A · rs757067036 · VCV1512960
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0111%, eas)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.044 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -3.3, phastCons 0.94 |
| Overall | ||
| CADD | 11.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0111%
East Asian · 5/44,882 alleles
Filtering AF
0.00434%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.00149%
24/1,613,932 alleles · ultra-rare
exomes 20/1,461,840 · genomes 4/152,092 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0111% | 8,976 |
| Admixed American | 0.00667% | 14,999 |
| European (non-Finnish) | 0.00119% | 84,284 |
| South Asian | 0.0011% | 91,084 |
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.Ser9=
- Coding
- c.27G>A
- MANE Select
- NM_004531
- dbSNP
- rs757067036
- Type
- single nucleotide variant
- Location
- chr5:53107148 (GRCh38)
- Gene constraint
- LOEUF 1.066 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.07 · 2 PDB
- Residue 9
- a β-strand; a UniProt-annotated variant site (in mocodb1)
Similar variants
- MOCS2 p.Ser9Leu Likely benign ★★ same residue
- MOCS2 p.Ser9Trp Likely benign ★ ⚠ same residue
- MOCS2 p.Ala49Gly Uncertain significance ★★ same condition
- MOCS2 p.Arg60His Uncertain significance ★★ same condition
- MOCS2 p.Asn81Tyr Uncertain significance ★★ ⚠ same condition
- MOCS2 p.Thr175Ala Uncertain significance ★★ ⚠ same condition
- MOCS2 p.Thr19Arg Uncertain significance ★★ same condition
- MOCS2 p.Pro22Leu Likely benign ★★ 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-ser9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown