SRC p.Ala378=
c.1134G>A · rs56408406 · VCV777573
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.84%, 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 -9.1 | GERP -4.2 |
| Overall | ||
| CADD | 0.274 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.84%
African / African-American · 1,379/75,022 alleles
Filtering AF
1.76%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.72%
Overall
0.0985%
1,590/1,613,756 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.84% | 54 |
| Admixed American | 0.11% | 907 |
| Remaining individualsnot grpmax-eligible | 0.0736% | 1,358 |
| European (non-Finnish) | 0.00822% | 12,164 |
| East Asian | 0.00223% | 44,870 |
| South Asian | 0.0011% | 91,060 |
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.Ala378=
- Coding
- c.1134G>A
- MANE Select
- NM_198291
- dbSNP
- rs56408406
- Type
- single nucleotide variant
- Location
- chr20:37402452 (GRCh38)
- Gene constraint
- LOEUF 0.383 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.59 · 79 PDB
- Residue 378
- the protein kinase domain; an α-helix
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-ala378 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown