ATF7IP p.Leu457=
c.1371C>T · rs61754405 · VCV2642754
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.415%, nfe)
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 -0.64 | GERP -2, phastCons 0.005 |
| Overall | ||
| CADD | 2.609 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.415%
European (non-Finnish) · 4,876/1,176,264 alleles
Filtering AF
0.405%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.401%
Overall
0.344%
5,518/1,602,068 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.415% | 241 |
| Ashkenazi Jewishnot grpmax-eligible | 0.338% | 295 |
| Finnishnot grpmax-eligible | 0.321% | 311 |
| Remaining individualsnot grpmax-eligible | 0.255% | 392 |
| Middle Eastern | 0.151% | 663 |
| Admixed American | 0.135% | 739 |
| African / African-American | 0.0674% | 1,484 |
| South Asian | 0.051% | 1,962 |
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
- ATF7IP
- Protein
- p.Leu457=
- Coding
- c.1371C>T
- MANE Select
- NM_018179
- dbSNP
- rs61754405
- Type
- single nucleotide variant
- Location
- chr12:14425286 (GRCh38)
- Gene constraint
- LOEUF 0.294 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 48.39 · 1 PDB
- Residue 457
- the 'disordered' region
Similar variants
- ATF7IP p.Ala1069Thr Benign ★★ same type
- ATF7IP p.Leu149= Benign ★★ same type
- ATF7IP p.Lys530Arg Benign ★★ ⚠ same type
- ATF7IP p.Met573Ile Likely benign ★★ same type
- ATF7IP p.Ser502Leu Likely benign ★★ same type
- ATF7IP p.Ser734Asn Benign ★★ ⚠ same type
- ATF7IP c.1559-2A>G Uncertain significance ★ same type
- ATF7IP p.Ala1191Val 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/atf7ip-p-leu457 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown