ATRN p.Cys993=
c.2979T>C · rs2514581567 · VCV1967216
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,614,092)
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 -0.2 | GERP -3.9, phastCons 0.47 |
| Overall | ||
| CADD | 6.931 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,614,092). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- ATRN
- Protein
- p.Cys993=
- Coding
- c.2979T>C
- MANE Select
- NM_139321
- dbSNP
- rs2514581567
- Type
- single nucleotide variant
- Location
- chr20:3584675 (GRCh38)
- Gene constraint
- LOEUF 0.395 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.27
- Residue 993
- the psi 4 domain
Similar variants
- ATRN p.Ala438Gly Uncertain significance ★★ ⚠ same type
- ATRN p.Ala87Val Uncertain significance ★★ ⚠ same type
- ATRN p.Arg1417Gln Uncertain significance ★★ ⚠ same type
- ATRN p.Arg173His Uncertain significance ★★ ⚠ same type
- ATRN p.Asn1035Ser Uncertain significance ★★ ⚠ same type
- ATRN p.Asn213Ser Uncertain significance ★★ ⚠ same type
- ATRN p.Asn300Thr Uncertain significance ★★ ⚠ same type
- ATRN p.Asp508Asn 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/atrn-p-cys993 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown