Is RET p.Ala479= (c.1437C>T) pathogenic?

RET p.Ala479= (c.1437C>T) is classified Benign/Likely benign in RET (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-02-03). Ultra-rare (popmax 0.0733%, amr); Associated with hereditary neoplastic syndrome.

What condition is associated with RET p.Ala479= (c.1437C>T)?

RET p.Ala479= (c.1437C>T) is associated with hereditary neoplastic syndrome, multiple endocrine neoplasia type 2B, multiple endocrine neoplasia type 2A (ClinVar).

How common is RET p.Ala479= (c.1437C>T) in the general population?

RET p.Ala479= (c.1437C>T) is ultra-rare (popmax 0.0733%, amr) (gnomAD).

RET p.Ala479=

c.1437C>T · rs576806356 · VCV136100

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0733%, amr)

Conditions

hereditary neoplastic syndrome

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 -4.5	GERP -4.3
Overall
CADD	2.3	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0733% Admixed American · 44/60,030 alleles

Filtering AF 0.0561% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.05%

Overall 0.0044% 71/1,614,000 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0733%	1,364
Remaining individualsnot grpmax-eligible	0.0064%	15,627
African / African-American	0.00533%	18,763
European (non-Finnish)	0.00153%	65,557
South Asian	0.0011%	91,082

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: RET
Protein: p.Ala479=
Coding: c.1437C>T
MANE Select: NM_020975
dbSNP: rs576806356
Type: single nucleotide variant
Location: chr10:43111380 (GRCh38)
Gene constraint: LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.27 · 34 PDB
Residue 479: the 'cadherin-like region 4 (cld4)' region

Full RET gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: multiple endocrine neoplasia type 2B multiple endocrine neoplasia type 2A multiple endocrine neoplasia type 2

Similar variants

RET c.1759+1G>A Pathogenic/Likely pathogenic ★★ same condition
RET c.1879+1G>A Pathogenic/Likely pathogenic ★★ same condition
RET p.Arg180Ter Pathogenic ★★ same condition
RET p.Arg77Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
RET p.Arg873Trp Likely pathogenic ★★ same condition
RET p.Arg897Ter Pathogenic ★★ same condition
RET p.Asp631Tyr Pathogenic ★★ ⚠ same condition
RET p.Cys609Arg 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-ala479 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown