SRC p.Phe408=
c.1224T>C · rs112739878 · VCV734030
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.99%, 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 -8.9 | GERP -4.2 |
| Overall | ||
| CADD | 1.556 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.99%
African / African-American · 1,494/74,982 alleles
Filtering AF
1.91%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.87%
Overall
0.104%
1,671/1,613,934 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.99% | 50 |
| Remaining individualsnot grpmax-eligible | 0.118% | 845 |
| Admixed American | 0.0967% | 1,034 |
| Middle Eastern | 0.0826% | 1,211 |
| South Asian | 0.00439% | 22,763 |
| European (non-Finnish) | 0.00305% | 32,777 |
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
- SRC
- Protein
- p.Phe408=
- Coding
- c.1224T>C
- MANE Select
- NM_198291
- dbSNP
- rs112739878
- Type
- single nucleotide variant
- Location
- chr20:37402542 (GRCh38)
- Gene constraint
- LOEUF 0.383 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.59 · 79 PDB
- Residue 408
- the protein kinase domain
Similar variants
- SRC p.Glu527Lys Pathogenic/Likely pathogenic ★★ same type
- SRC p.Glu492Lys Uncertain significance ★★ ⚠ same type
- SRC c.1117-180C>T Benign ★★ same type
- SRC c.1117-9C>T Likely benign ★★ same type
- SRC c.1271-55= Benign ★★ same type
- SRC c.449+9C>T Benign/Likely benign ★★ same type
- SRC c.553+8C>T Benign/Likely benign ★★ same type
- SRC c.554-5C>T Benign ★★ 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/src-p-phe408 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown