Is RET p.Pro162His (c.485C>A) pathogenic?

RET p.Pro162His (c.485C>A) is classified Uncertain significance in RET (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-06-21). AlphaMissense: likely benign (0.2401); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with RET p.Pro162His (c.485C>A)?

RET p.Pro162His (c.485C>A) is associated with hereditary neoplastic syndrome, multiple endocrine neoplasia type 2 (ClinVar).

How common is RET p.Pro162His (c.485C>A) in the general population?

RET p.Pro162His (c.485C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about RET p.Pro162His (c.485C>A)?

AlphaMissense predicts likely benign (score 0.2401) — an in-silico prediction, not a clinical call.

RET p.Pro162His

c.485C>A · rs1205703835 · VCV1480894

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2401 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.2401	likely benign
REVEL	0.207	benign-leaning
SaProt	LLR -7.72	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.9	GERP 1.7, phastCons 0.41
Regional constraint	o/e 0.88	unconstrained · MANE · 17 kb · p 0.00012 · regional, not allelic
Overall
CADD	19.23	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Pro162His
Coding: c.485C>A
MANE Select: NM_020975
dbSNP: rs1205703835
Type: single nucleotide variant
Location: chr10:43102489 (GRCh38)
Gene constraint: LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.27 · 34 PDB
Residue 162: an α-helix

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 2

Similar variants

RET p.Pro162Ala Uncertain significance ★★ ⚠ same residue
RET p.Pro162Arg Uncertain significance ★★ ⚠ same residue
RET p.Pro162Leu Uncertain significance ★★ ⚠ same residue
RET p.Pro162Ser Uncertain significance ★★ ⚠ same residue
RET p.Pro162Thr Uncertain significance ★★ ⚠ same residue
RET p.Pro162= Likely benign ★ same residue
RET c.1759+1G>A Pathogenic/Likely pathogenic ★★ same condition
RET c.1879+1G>A 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-pro162his (accessed [today's date]).

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