PFKL p.Arg151=
c.453G>C · rs1465747037 · VCV3061136
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Conditions
1
PFKL-related disorder
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 3.7 | GERP 0.57, phastCons 1 |
| Overall | ||
| CADD | 4.102 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,082 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000558%
9/1,612,922 alleles · ultra-rare
exomes 8/1,460,750 · genomes 1/152,172 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,082 |
| Admixed American | 0.00167% | 59,996 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,458 |
| European (non-Finnish) | 0.000509% | 196,653 |
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
- PFKL
- Protein
- p.Arg151=
- Coding
- c.453G>C
- MANE Select
- NM_002626
- dbSNP
- rs1465747037
- Type
- single nucleotide variant
- Location
- chr21:44313003 (GRCh38)
- Gene constraint
- LOEUF 1.028 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.53 · 5 PDB
- Residue 151
- the 'n-terminal catalytic pfk domain 1' region; a UniProt-annotated variant site (in)
Disease context
PFKL-related disorder
Similar variants
- PFKL p.Arg151Gln Likely benign ★ same residue
- PFKL c.1410-5T>C Likely benign same condition
- PFKL c.86-818C>T Benign same condition
- PFKL p.Ala417= Likely benign same condition
- PFKL p.Asn531= Likely benign same condition
- PFKL p.Asp705Glu Likely benign same condition
- PFKL p.Pro329= Likely benign same condition
- PFKL p.Tyr761= Likely benign 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/pfkl-p-arg151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown