MERTK p.Ser397=
c.1191T>C · rs2104741150 · VCV1154193
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.21 | acceptor loss, 3 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -2.8 |
| Overall | ||
| CADD | 1.101 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,956 alleles
Overall
6.84e-05%
1/1,461,800 alleles · very rare
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
- MERTK
- Protein
- p.Ser397=
- Coding
- c.1191T>C
- MANE Select
- NM_006343
- dbSNP
- rs2104741150
- Type
- single nucleotide variant
- Location
- chr2:111982888 (GRCh38)
- Gene constraint
- LOEUF 0.787 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.78 · 42 PDB
- Residue 397
- a β-strand; the fibronectin type-iii 2 domain
Similar variants
- MERTK c.1296+1G>A Pathogenic/Likely pathogenic ★★ same type
- MERTK c.1605-2A>G Pathogenic ★★ same type
- MERTK c.1787-2A>T Pathogenic/Likely pathogenic ★★ same type
- MERTK c.1867+1G>A Likely pathogenic ★★ same type
- MERTK c.1868-1G>A Pathogenic ★★ same type
- MERTK c.2189+1G>T Pathogenic ★★ same type
- MERTK p.Ala768Thr Pathogenic/Likely pathogenic ★★ same type
- MERTK p.Ala768Val 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/mertk-p-ser397 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown