LARP7 p.Phe77=
c.231T>C · rs2048240719 · VCV1530006
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00251%, 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 0.63 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 9.176 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00251%
European (non-Finnish) · 29/1,155,264 alleles
Filtering AF
0.00176%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00152%
Overall
0.00189%
30/1,584,780 alleles · very rare
exomes 28/1,432,576 · genomes 2/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00251% | 39,837 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,420 |
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.Phe77=
- Coding
- c.231T>C
- MANE Select
- NM_016648
- dbSNP
- rs2048240719
- Type
- single nucleotide variant
- Location
- chr4:112646379 (GRCh38)
- Gene constraint
- LOEUF 1.129 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.89 · 5 PDB
- Residue 77
- the hth la-type rna-binding domain
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-phe77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown