SRRT p.Ile557=
c.1671C>A · rs755043116 · VCV721796
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.153%, 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 0.013 | GERP -2.2, phastCons 0.036 |
| Overall | ||
| CADD | 7.445 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.153%
Admixed American · 92/60,016 alleles
Filtering AF
0.128%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.119%
Overall
0.00576%
93/1,614,072 alleles · rare
exomes 83/1,461,866 · genomes 10/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.153% | 652 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
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
- SRRT
- Protein
- p.Ile557=
- Coding
- c.1671C>A
- MANE Select
- NM_015908
- dbSNP
- rs755043116
- Type
- single nucleotide variant
- Location
- chr7:100886818 (GRCh38)
- Gene constraint
- LOEUF 0.404 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.61 · 6 PDB
- Residue 557
- an α-helix
Similar variants
- SRRT c.1042-18C>G Benign ★★ same type
- SRRT c.1042-7C>T Benign ★★ same type
- SRRT c.2556-9A>T Benign ★★ same type
- SRRT p.Arg518= Benign ★★ same type
- SRRT p.Glu205= Benign ★★ same type
- SRRT p.Leu157= Benign ★★ same type
- SRRT p.Leu265= Benign ★★ same type
- SRRT p.Ala190Val 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/srrt-p-ile557 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown