CMYA5 p.Ser543=
c.1629C>T · rs141358383 · VCV2655558
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.421%, eas)
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 -0.57 | GERP -0.5, phastCons 0.012 |
| Overall | ||
| CADD | 5.503 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.421%
East Asian · 189/44,882 alleles
Filtering AF
0.372%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.353%
Overall
0.0248%
400/1,613,820 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.421% | 237 |
| South Asian | 0.143% | 701 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,499 |
| African / African-American | 0.0373% | 2,679 |
| Middle Eastern | 0.033% | 3,030 |
| Admixed American | 0.01% | 10,002 |
| European (non-Finnish) | 0.0017% | 58,993 |
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
- CMYA5
- Protein
- p.Ser543=
- Coding
- c.1629C>T
- MANE Select
- NM_153610
- dbSNP
- rs141358383
- Type
- single nucleotide variant
- Location
- chr5:79730394 (GRCh38)
- Gene constraint
- LOEUF 0.807 · pLI <0.01 (gnomAD)
- Residue 543
- the 'disordered' region
Similar variants
- CMYA5 p.Gln1229His Uncertain significance ★★ ⚠ same type
- CMYA5 p.Pro1256Leu Uncertain significance ★★ ⚠ same type
- CMYA5 p.Ala2958Ser Likely benign ★★ same type
- CMYA5 p.Arg147Gln Benign ★★ same type
- CMYA5 p.Asp3147Tyr Benign/Likely benign ★★ same type
- CMYA5 p.Asp53Glu Likely benign ★★ same type
- CMYA5 p.Asp836= Benign ★★ same type
- CMYA5 p.Gln1111= Benign/Likely 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/cmya5-p-ser543 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown