MUC1 p.Ser38=
c.114G>C · VCV4913702
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -1.2 | GERP -1.9 |
| Overall | ||
| CADD | 1.883 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,080 alleles
Filtering AF
0.00188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00164%
Overall
0.00217%
35/1,613,480 alleles · ultra-rare
exomes 32/1,461,500 · genomes 3/151,980 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,080 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,233 |
| European (non-Finnish) | 0.00263% | 38,058 |
| Admixed American | 0.00167% | 59,970 |
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
- MUC1
- Protein
- p.Ser38=
- Coding
- c.114G>C
- Type
- single nucleotide variant
- Location
- chr1:155192228 (GRCh38)
- Gene constraint
- LOEUF 0.964 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 47.92 · 23 PDB
- Residue 38
- the 'disordered' region
Similar variants
- MUC1 p.Ser38Phe Uncertain significance ★ same residue
- MUC1 p.Ser38fs Likely pathogenic ★ same residue
- MUC1 p.Val127Ile Uncertain significance ★★ same type
- MUC1 c.159+219A>G Likely benign ★★ same type
- MUC1 c.160-52C>G Likely benign ★★ same type
- MUC1 p.Ser1032Thr Likely benign ★★ same type
- MUC1 p.Thr31= Benign ★★ same type
- MUC1 c.1354-1G>A Likely pathogenic ★ 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/muc1-p-ser38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown