GFER p.Asp192=
c.576T>C · rs968617998 · VCV2031093
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000508%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.4 | GERP -3.1 |
| Overall | ||
| CADD | 10.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000508%
European (non-Finnish) · 6/1,180,006 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000372%
6/1,613,098 alleles · very rare
exomes 6/1,460,752 · genomes 0/152,346 · 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.Asp192=
- Coding
- c.576T>C
- MANE Select
- NM_005262
- dbSNP
- rs968617998
- Type
- single nucleotide variant
- Location
- chr16:1985986 (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 192
- the erv/alr sulfhydryl oxidase domain
Similar variants
- GFER p.Asp192Gly Pathogenic same residue
- 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
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-asp192 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown