DFFA p.Thr300=
c.900G>A · rs78256349 · VCV782903
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.24%, afr)
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 -3.4 | GERP -3.2 |
| Overall | ||
| CADD | 1.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.24%
African / African-American · 934/75,064 alleles
Filtering AF
1.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.15%
Overall
0.0864%
1,394/1,614,232 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.24% | 80 |
| Middle Eastern | 0.247% | 404 |
| Ashkenazi Jewishnot grpmax-eligible | 0.213% | 470 |
| Remaining individualsnot grpmax-eligible | 0.134% | 744 |
| Admixed American | 0.102% | 984 |
| Finnishnot grpmax-eligible | 0.0515% | 1,941 |
| South Asian | 0.0209% | 4,794 |
| European (non-Finnish) | 0.0155% | 6,448 |
| East Asian | 0.00446% | 22,439 |
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
- DFFA
- Protein
- p.Thr300=
- Coding
- c.900G>A
- MANE Select
- NM_004401
- dbSNP
- rs78256349
- Type
- single nucleotide variant
- Location
- chr1:10461586 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.25 · 3 PDB
- Residue 300
- an α-helix
Similar variants
- DFFA p.Arg296Cys Likely benign ★★ ⚠ same type
- DFFA p.Cys165Arg Benign ★★ same type
- DFFA p.Ala236Val Uncertain significance ★ ⚠ same type
- DFFA p.Ala250Pro Uncertain significance ★ ⚠ same type
- DFFA p.Ala250Ser Uncertain significance ★ ⚠ same type
- DFFA p.Ala294Thr Uncertain significance ★ ⚠ same type
- DFFA p.Ala51Pro Uncertain significance ★ ⚠ same type
- DFFA p.Ala7Val 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/dffa-p-thr300 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown