LARP7 p.Phe451=
c.1353C>T · rs765596788 · VCV2165277
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.058 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.91 | GERP -3.3, phastCons 0.003 |
| Overall | ||
| CADD | 10.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,858 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000313%
Overall
0.00093%
15/1,613,568 alleles · very rare
exomes 15/1,461,524 · genomes 0/152,044 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,429 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,245 |
| African / African-American | 0.00133% | 74,942 |
| European (non-Finnish) | 0.000848% | 117,972 |
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
- LARP7
- Protein
- p.Phe451=
- Coding
- c.1353C>T
- MANE Select
- NM_016648
- dbSNP
- rs765596788
- Type
- single nucleotide variant
- Location
- chr4:112650519 (GRCh38)
- Gene constraint
- LOEUF 1.129 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.89 · 5 PDB
- Residue 451
- the xrrm domain; an α-helix
Similar variants
- LARP7 c.1295-2A>G Likely pathogenic ★★ same type
- LARP7 p.Arg227Ter Pathogenic/Likely pathogenic ★★ same type
- LARP7 p.Arg309Ter Pathogenic/Likely pathogenic ★★ same type
- LARP7 p.Lys278Ter Likely pathogenic ★★ same type
- LARP7 p.Ser273Ter Pathogenic/Likely pathogenic ★★ same type
- LARP7 c.203-3T>G Uncertain significance ★★ same type
- LARP7 c.387+5G>C Uncertain significance ★★ same type
- LARP7 p.Ala324Thr 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/larp7-p-phe451 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown