GFER p.Ala62=
c.186C>G · rs763610770 · VCV2884979
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00218%, nfe)
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 -3.5 | GERP -2.4 |
| Overall | ||
| CADD | 8.754 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00218%
European (non-Finnish) · 25/1,146,266 alleles
Filtering AF
0.0015%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00126%
Overall
0.00162%
25/1,538,474 alleles · very rare
exomes 23/1,386,286 · genomes 2/152,188 · joint denominator
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
- GFER
- Protein
- p.Ala62=
- Coding
- c.186C>G
- MANE Select
- NM_005262
- dbSNP
- rs763610770
- Type
- single nucleotide variant
- Location
- chr16:1984404 (GRCh38)
- Gene constraint
- LOEUF 1.87 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.50 · 7 PDB
- Residue 62
- the 'disordered' region
Similar variants
- GFER p.Arg194His Pathogenic ★★ same type
- GFER p.Ser189Ter Pathogenic ★★ same type
- GFER c.258+1G>A Uncertain significance ★★ same type
- GFER p.Ala45Thr Uncertain significance ★★ ⚠ same type
- GFER p.Ala46Val Uncertain significance ★★ ⚠ same type
- GFER p.Ala73Ser Uncertain significance ★★ ⚠ same type
- GFER p.Arg196Cys Uncertain significance ★★ ⚠ same type
- GFER p.Arg82Gln 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/gfer-p-ala62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown