SLC39A4 p.Cys603=
c.1809C>T · rs1554871900 · VCV2955432
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.32 | GERP -3.5, phastCons 0.86 |
| Overall | ||
| CADD | 10.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,036 alleles
Overall
6.2e-05%
1/1,613,208 alleles · very rare
exomes 1/1,460,904 · genomes 0/152,304 · joint denominator
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
- SLC39A4
- Protein
- p.Cys603=
- Coding
- c.1809C>T
- MANE Select
- NM_130849
- dbSNP
- rs1554871900
- Type
- single nucleotide variant
- Location
- chr8:144412765 (GRCh38)
- Gene constraint
- LOEUF 1.262 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.05
Similar variants
- SLC39A4 c.1149+1G>A Likely pathogenic ★★ same type
- SLC39A4 c.1287+1G>A Likely pathogenic ★★ same type
- SLC39A4 c.1287+2T>C Likely pathogenic ★★ same type
- SLC39A4 c.1628-2A>G Likely pathogenic ★★ same type
- SLC39A4 c.192+19G>A Pathogenic/Likely pathogenic ★★ same type
- SLC39A4 c.193-2A>G Likely pathogenic ★★ same type
- SLC39A4 c.475-2A>G Pathogenic/Likely pathogenic ★★ same type
- SLC39A4 c.667+1G>T 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/slc39a4-p-cys603 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown