ELFN2 p.Asn236=
c.708C>T · VCV3844419
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.08%, amr)
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 -2.2 | GERP -4.2 |
| Overall | ||
| CADD | 5.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.08%
Admixed American · 48/59,988 alleles
Filtering AF
0.0619%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0556%
Overall
0.00504%
81/1,607,094 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.08% | 1,250 |
| Middle Eastern | 0.0164% | 6,084 |
| East Asian | 0.0134% | 7,482 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,606 |
| European (non-Finnish) | 0.00186% | 53,628 |
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
- ELFN2
- Protein
- p.Asn236=
- Coding
- c.708C>T
- MANE Select
- NM_052906
- Type
- single nucleotide variant
- Location
- chr22:37374827 (GRCh38)
- Gene constraint
- LOEUF 0.566 · pLI 0.72 (gnomAD)
- Structure
- AlphaFold pLDDT 61.79
- Residue 236
- the lrrct domain
Similar variants
- ELFN2 p.Asn76Ser Benign ★★ same type
- ELFN2 p.Ser262Tyr Benign ★★ same type
- ELFN2 p.Ala183Thr Uncertain significance ★ ⚠ same type
- ELFN2 p.Ala198Val Uncertain significance ★ ⚠ same type
- ELFN2 p.Ala243Gly Uncertain significance ★ ⚠ same type
- ELFN2 p.Ala265Thr Uncertain significance ★ ⚠ same type
- ELFN2 p.Ala455Thr Uncertain significance ★ ⚠ same type
- ELFN2 p.Ala484Thr 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/elfn2-p-asn236 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown