RELT p.Ala160=
c.480C>T · rs35329118 · VCV2642142
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.412%, mid)
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 -8.7 | GERP -4.4 |
| Overall | ||
| CADD | 0.228 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.412%
Middle Eastern · 25/6,062 alleles
Filtering AF
0.287%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.245%
Overall
0.19%
3,061/1,613,638 alleles · rare
exomes 2,792/1,461,330 · genomes 269/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.412% | 242 |
| Finnishnot grpmax-eligible | 0.355% | 282 |
| European (non-Finnish) | 0.216% | 463 |
| Remaining individualsnot grpmax-eligible | 0.144% | 694 |
| Admixed American | 0.112% | 896 |
| South Asian | 0.0626% | 1,598 |
| African / African-American | 0.0453% | 2,207 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0406% | 2,466 |
| East Asian | 0.00223% | 44,872 |
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
- RELT
- Protein
- p.Ala160=
- Coding
- c.480C>T
- MANE Select
- NM_152222
- dbSNP
- rs35329118
- Type
- single nucleotide variant
- Location
- chr11:73392323 (GRCh38)
- Gene constraint
- LOEUF 0.955 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.38
Similar variants
- RELT p.Asp87Val Likely pathogenic ★ same type
- RELT p.Leu174Arg Likely pathogenic ★ same type
- RELT c.287+1G>T Uncertain significance ★ same type
- RELT p.Ala136Val Uncertain significance ★ ⚠ same type
- RELT p.Ala164Thr Uncertain significance ★ ⚠ same type
- RELT p.Ala164Val Uncertain significance ★ ⚠ same type
- RELT p.Ala239Val Uncertain significance ★ ⚠ same type
- RELT p.Ala267Val 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/relt-p-ala160 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown