EMG1 p.Ser5=
c.15T>C · rs149578211 · VCV714059
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.91%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.19 | GERP -3.1, phastCons 0.68 |
| Overall | ||
| CADD | 5.718 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.91%
African / African-American · 2,933/74,990 alleles
Filtering AF
3.79%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.75%
Overall
0.222%
3,580/1,613,020 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.91% | 26 |
| Remaining individualsnot grpmax-eligible | 0.309% | 324 |
| Admixed American | 0.274% | 365 |
| Middle Eastern | 0.132% | 758 |
| European (non-Finnish) | 0.0231% | 4,336 |
| South Asian | 0.011% | 9,086 |
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
- EMG1
- Protein
- p.Ser5=
- Coding
- c.15T>C
- MANE Select
- NM_006331
- dbSNP
- rs149578211
- Type
- single nucleotide variant
- Location
- chr12:6970938 (GRCh38)
- Gene constraint
- LOEUF 1.228 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.38 · 4 PDB
- Residue 5
- a modified residue (phosphoserine); the 'disordered' region
Similar variants
- EMG1 p.Ala34Gly Benign ★★ same type
- EMG1 p.Arg13Leu Benign/Likely benign ★★ same type
- EMG1 p.Cys171= Benign ★★ same type
- EMG1 p.Ser192= Benign ★★ same type
- LPCAT3 p.Tyr137= Benign ★★ same type
- EMG1 p.Ala19Gly Uncertain significance ★ ⚠ same type
- EMG1 p.Gln139Arg Uncertain significance ★ ⚠ same type
- EMG1 p.Gln20Arg Uncertain significance ★ ⚠ same type
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/emg1-p-ser5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown