ELF1 p.Pro364=
c.1092A>T · rs151034333 · VCV771190
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.44%, sas)
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 -3.6 | GERP -3.3 |
| Overall | ||
| CADD | 0.306 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.44%
South Asian · 1,312/91,080 alleles
Filtering AF
1.38%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.35%
Overall
0.83%
13,393/1,614,202 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.44% | 69 |
| Ashkenazi Jewishnot grpmax-eligible | 1.24% | 81 |
| Amishnot grpmax-eligible | 0.987% | 101 |
| European (non-Finnish) | 0.887% | 113 |
| Finnishnot grpmax-eligible | 0.771% | 130 |
| Remaining individualsnot grpmax-eligible | 0.659% | 152 |
| Middle Eastern | 0.33% | 303 |
| Admixed American | 0.317% | 316 |
| African / African-American | 0.167% | 600 |
| East Asian | 0.00446% | 22,440 |
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
- ELF1
- Protein
- p.Pro364=
- Coding
- c.1092A>T
- MANE Select
- NM_032377 · reported on NM_172373
- dbSNP
- rs151034333
- Type
- single nucleotide variant
- Location
- chr13:40941085 (GRCh38)
- Structure
- AlphaFold pLDDT 85.98 · 7 PDB
Similar variants
- ELF1 p.Leu614= Benign ★★ same type
- ELF1 p.Ala29Thr Uncertain significance ★ ⚠ same type
- ELF1 p.Ala353Ser Uncertain significance ★ ⚠ same type
- ELF1 p.Ala459Val Uncertain significance ★ ⚠ same type
- ELF1 p.Arg323Thr Uncertain significance ★ ⚠ same type
- ELF1 p.Arg328Gln Uncertain significance ★ ⚠ same type
- ELF1 p.Arg330Lys Uncertain significance ★ ⚠ same type
- ELF1 p.Arg369Lys 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/elf1-p-pro364 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown