F13A1 p.Pro384=
c.1152T>C · rs375255557 · VCV765345
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0175%, 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 -3.6 | GERP -4.8 |
| Overall | ||
| CADD | 1.549 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0175%
European (non-Finnish) · 207/1,180,048 alleles
Filtering AF
0.0155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0148%
Overall
0.013%
210/1,614,126 alleles · ultra-rare
exomes 202/1,461,858 · genomes 8/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0175% | 5,701 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
| African / African-American | 0.00133% | 74,956 |
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
- F13A1
- Protein
- p.Pro384=
- Coding
- c.1152T>C
- MANE Select
- NM_000129
- dbSNP
- rs375255557
- Type
- single nucleotide variant
- Location
- chr6:6197287 (GRCh38)
- Gene constraint
- LOEUF 0.734 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.15 · 15 PDB
- Residue 384
- a β-strand
Similar variants
- F13A1 c.691-1G>A Pathogenic/Likely pathogenic ★★ same type
- F13A1 p.Arg327Gln Pathogenic/Likely pathogenic ★★ same type
- F13A1 p.Arg409Gln Likely pathogenic ★★ ⚠ same type
- F13A1 p.Arg662Ter Pathogenic ★★ same type
- F13A1 p.Arg682His Pathogenic ★★ ⚠ same type
- F13A1 p.Arg78Cys Pathogenic/Likely pathogenic ★★ same type
- F13A1 p.Gly274Arg Likely pathogenic ★★ same type
- F13A1 c.*1045C>G 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/f13a1-p-pro384 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown