F5 p.His1673=
c.5019T>C · rs373570992 · VCV1744799
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00297%, nfe)
Conditions
1
Inborn genetic diseases
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 -1.1 | GERP -3.1 |
| Overall | ||
| CADD | 1.271 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00297%
European (non-Finnish) · 35/1,179,814 alleles
Filtering AF
0.00215%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00191%
Overall
0.00217%
35/1,613,798 alleles · very rare
exomes 35/1,461,460 · genomes 0/152,338 · 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
- F5
- Protein
- p.His1673=
- Coding
- c.5019T>C
- MANE Select
- NM_000130
- dbSNP
- rs373570992
- Type
- single nucleotide variant
- Location
- chr1:169530975 (GRCh38)
- Gene constraint
- LOEUF 0.704 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.57 · 23 PDB
- Residue 1673
- a β-strand; the f5/8 type a 3 domain; the plastocyanin-like 5 domain
Similar variants
- F5 p.His1673Tyr Uncertain significance ★ same residue
- F5 p.Arg441His Uncertain significance ★★ ⚠ same condition
- F5 p.Asn1559Ser Uncertain significance ★★ ⚠ same condition
- F5 p.Asn1575Ser Uncertain significance ★★ ⚠ same condition
- F5 p.Asp1739Gly Uncertain significance ★★ ⚠ same condition
- F5 p.Glu2029Asp Uncertain significance ★★ ⚠ same condition
- F5 p.Glu48Gln Uncertain significance ★★ ⚠ same condition
- F5 p.His812Tyr Uncertain significance ★★ ⚠ 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/f5-p-his1673 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown