AFG2A p.Ile164=
c.492C>A · rs991945925 · VCV795796
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00535%, afr)
Conditions
1
microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome
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 0.2 | GERP -2.9, phastCons 0.99 |
| Overall | ||
| CADD | 7.848 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00535%
African / African-American · 4/74,774 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.000248%
4/1,611,376 alleles · very rare
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
- AFG2A
- Protein
- p.Ile164=
- Coding
- c.492C>A
- MANE Select
- NM_145207
- dbSNP
- rs991945925
- Type
- single nucleotide variant
- Location
- chr4:122933484 (GRCh38)
- Structure
- AlphaFold pLDDT 73.21 · 2 PDB
- Residue 164
- the 'required for interaction with afg2b and cinp' region; a UniProt-annotated variant site (in nedhsb)
Similar variants
- AFG2A c.1714+1G>A Pathogenic ★★ same condition
- AFG2A c.446+1G>A Likely pathogenic ★★ same condition
- AFG2A p.Ala844Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
- AFG2A p.Arg445Ter Pathogenic/Likely pathogenic ★★ same condition
- AFG2A p.Arg510Ter Pathogenic/Likely pathogenic ★★ same condition
- AFG2A p.Arg514Ter Pathogenic/Likely pathogenic ★★ same condition
- AFG2A p.Arg538Ter Pathogenic/Likely pathogenic ★★ same condition
- AFG2A p.Arg655Ter 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/afg2a-p-ile164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown