EMC1 p.Val62=
c.186G>A · rs775306558 · VCV2441216
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00988%, sas)
Conditions
1
cerebellar atrophy, visual impairment, and psychomotor retardation;
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.32 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4 | GERP 0.92, phastCons 1 |
| Overall | ||
| CADD | 17.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00988%
South Asian · 9/91,074 alleles
Filtering AF
0.00514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00375%
Overall
0.000684%
10/1,461,672 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00988% | 10,119 |
| European (non-Finnish) | 8.48e-05% | 1,179,884 |
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
- EMC1
- Protein
- p.Val62=
- Coding
- c.186G>A
- MANE Select
- NM_015047
- dbSNP
- rs775306558
- Type
- single nucleotide variant
- Location
- chr1:19244940 (GRCh38)
- Gene constraint
- LOEUF 0.913 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.67 · 10 PDB
- Residue 62
- a β-strand
Similar variants
- EMC1 p.Val62Met Uncertain significance ★ ⚠ same residue
- EMC1 c.287-1G>A Likely pathogenic ★★ same condition
- EMC1 c.787-1G>A Likely pathogenic ★★ same condition
- EMC1 p.Arg660Ter Pathogenic/Likely pathogenic ★★ same condition
- EMC1 p.Arg69Ter Pathogenic/Likely pathogenic ★★ same condition
- EMC1 p.Leu266Ter Pathogenic/Likely pathogenic ★★ same condition
- EMC1 p.Met1Arg Pathogenic/Likely pathogenic ★★ same condition
- EMC1 p.Thr82Met Pathogenic/Likely 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/emc1-p-val62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown