SRRT p.Arg518=
c.1554C>G · rs149979693 · VCV716358
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.18%, afr)
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 2.7 | GERP -0.79, phastCons 1 |
| Overall | ||
| CADD | 11.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.18%
African / African-American · 887/75,010 alleles
Filtering AF
1.12%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.09%
Overall
0.0612%
987/1,613,830 alleles · low-frequency
exomes 480/1,461,566 · genomes 507/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.18% | 85 |
| Remaining individualsnot grpmax-eligible | 0.088% | 1,136 |
| Admixed American | 0.055% | 1,819 |
| Middle Eastern | 0.0343% | 2,918 |
| South Asian | 0.0011% | 91,062 |
| European (non-Finnish) | 0.000763% | 131,113 |
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.Arg518=
- Coding
- c.1554C>G
- MANE Select
- NM_015908
- dbSNP
- rs149979693
- Type
- single nucleotide variant
- Location
- chr7:100886342 (GRCh38)
- Gene constraint
- LOEUF 0.404 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.61 · 6 PDB
- Residue 518
- 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.Glu205= Benign ★★ same type
- SRRT p.Leu157= Benign ★★ same type
- SRRT p.Leu265= Benign ★★ same type
- SRRT p.Ala190Val Uncertain significance ★ ⚠ same type
- SRRT p.Ala245Gly 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-arg518 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown