NARS2 p.Pro24=
c.72T>G · rs138923107 · VCV1205348
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0799%, afr)
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 0.8 | GERP -1.6, phastCons 0.016 |
| Overall | ||
| CADD | 11.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0799%
African / African-American · 60/75,048 alleles
Filtering AF
0.0637%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0579%
Overall
0.00551%
89/1,614,162 alleles · ultra-rare
exomes 59/1,461,882 · genomes 30/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0799% | 1,251 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,814 |
| Admixed American | 0.0117% | 8,574 |
| European (non-Finnish) | 0.00119% | 84,287 |
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
- NARS2
- Protein
- p.Pro24=
- Coding
- c.72T>G
- MANE Select
- NM_024678
- dbSNP
- rs138923107
- Type
- single nucleotide variant
- Location
- chr11:78574417 (GRCh38)
- Gene constraint
- LOEUF 1.253 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.59
Similar variants
- NARS2 p.Pro24Ser Uncertain significance ★ ⚠ same residue
- NARS2 p.Arg140Ter Pathogenic ★★ same type
- NARS2 p.Arg243Ter Pathogenic/Likely pathogenic ★★ same type
- NARS2 p.Asn317= Pathogenic/Likely pathogenic ★★ same type
- NARS2 p.Tyr323Ter Pathogenic/Likely pathogenic ★★ same type
- NARS2 p.Tyr412Ter Pathogenic ★★ same type
- NARS2 c.689+6A>G Uncertain significance ★★ same type
- NARS2 p.Ala17Val 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/nars2-p-pro24 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown