RET p.Arg313=
c.939G>A · VCV3904560
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
multiple endocrine neoplasia type 2A
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 -0.042 | GERP -4, phastCons 0.18 |
| Overall | ||
| CADD | 7.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- RET
- Protein
- p.Arg313=
- Coding
- c.939G>A
- MANE Select
- NM_020975
- Type
- single nucleotide variant
- Location
- chr10:43106447 (GRCh38)
- Gene constraint
- LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.27 · 34 PDB
- Residue 313
- the 'cadherin-like region 3 (cld3)' region; a UniProt-annotated variant site (in hscr1)
Disease context
multiple endocrine neoplasia type 2A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Multiple endocrine neoplasia type 2 (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adolescent, Adult, Childhood, Infancy
- Prevalence
- 1-9 / 100 000 (Europe)
Similar variants
- RET p.Arg313Gln Uncertain significance ★★ ⚠ same residue
- RET p.Arg313Leu Uncertain significance ★★ ⚠ same residue
- RET p.Arg313Trp Uncertain significance ★★ ⚠ same residue
- RET p.Asp631Tyr Pathogenic ★★ ⚠ same condition
- RET p.Cys609Gly Pathogenic ★★ same condition
- RET p.Cys609Ser Pathogenic ★★ same condition
- RET p.Cys609Tyr Pathogenic ★★ same condition
- RET p.Cys611Arg Pathogenic/Likely pathogenic ★★ same condition
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/ret-p-arg313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown