ERGIC1 p.Arg12=
c.36G>A · VCV4250675
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
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 7.6 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 13.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,082 alleles
Filtering AF
0.0058%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00241%
Overall
0.000805%
13/1,614,000 alleles · ultra-rare
exomes 11/1,461,870 · genomes 2/152,130 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,041 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0203% | 4,935 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| European (non-Finnish) | 0.000339% | 295,007 |
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
- ERGIC1
- Protein
- p.Arg12=
- Coding
- c.36G>A
- MANE Select
- NM_001031711
- Type
- single nucleotide variant
- Location
- chr5:172888714 (GRCh38)
- Gene constraint
- LOEUF 0.683 · pLI 0.04 (gnomAD)
- Structure
- AlphaFold pLDDT 88.96
Similar variants
- ERGIC1 c.250+1G>A Likely pathogenic ★ same type
- ERGIC1 c.155+1G>A Uncertain significance ★ same type
- ERGIC1 p.Ala228Glu Uncertain significance ★ ⚠ same type
- ERGIC1 p.Ala267Thr Uncertain significance ★ ⚠ same type
- ERGIC1 p.Arg116Cys Uncertain significance ★ ⚠ same type
- ERGIC1 p.Arg232His Uncertain significance ★ ⚠ same type
- ERGIC1 p.Arg246Trp Uncertain significance ★ ⚠ same type
- ERGIC1 p.Asn180Ser 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/ergic1-p-arg12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown