CBLC p.Ser38=
c.114C>T · VCV4821149
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.363%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.60 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.52 | GERP 0.93 |
| Overall | ||
| CADD | 9.936 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.363%
South Asian · 331/91,064 alleles
Filtering AF
0.331%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.319%
Overall
0.026%
418/1,609,248 alleles · rare
exomes 397/1,456,984 · genomes 21/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.363% | 275 |
| Remaining individualsnot grpmax-eligible | 0.0448% | 2,230 |
| African / African-American | 0.00667% | 15,000 |
| European (non-Finnish) | 0.00424% | 23,593 |
| Finnishnot grpmax-eligible | 0.00335% | 29,865 |
| East Asian | 0.00223% | 44,840 |
| Admixed American | 0.00167% | 59,992 |
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
- CBLC
- Protein
- p.Ser38=
- Coding
- c.114C>T
- MANE Select
- NM_012116
- Type
- single nucleotide variant
- Location
- chr19:44778045 (GRCh38)
- Gene constraint
- LOEUF 1.058 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.85 · 7 PDB
- Residue 38
- the cbl-ptb domain; the '4h' region
Similar variants
- CBLC p.Ala122Ser Uncertain significance ★ ⚠ same type
- CBLC p.Ala137Val Uncertain significance ★ ⚠ same type
- CBLC p.Ala21Val Uncertain significance ★ ⚠ same type
- CBLC p.Ala377Pro Uncertain significance ★ same type
- CBLC p.Ala398Val Uncertain significance ★ ⚠ same type
- CBLC p.Ala433Ser Uncertain significance ★ ⚠ same type
- CBLC p.Ala450Gly Uncertain significance ★ ⚠ same type
- CBLC p.Ala465Val 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/cblc-p-ser38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown