Is MET p.Pro1033= (c.3099C>T) pathogenic?

MET p.Pro1033= (c.3099C>T) is classified Likely benign in MET (ClinVar, Multiple submitters, 2 submitters; last evaluated 2020-07-16). Absent from gnomAD v4.1; Associated with renal cell carcinoma.

What condition is associated with MET p.Pro1033= (c.3099C>T)?

MET p.Pro1033= (c.3099C>T) is associated with renal cell carcinoma, hereditary neoplastic syndrome (ClinVar).

How common is MET p.Pro1033= (c.3099C>T) in the general population?

MET p.Pro1033= (c.3099C>T) is absent from gnomAD v4.1 (gnomAD).

MET p.Pro1033=

c.3099C>T · rs754909964 · VCV724075

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

renal cell carcinoma

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 0.15	GERP 0.15, phastCons 0.93
Overall
CADD	8.55	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: MET
Protein: p.Pro1033=
Coding: c.3099C>T
MANE Select: NM_000245
dbSNP: rs754909964
Type: single nucleotide variant
Location: chr7:116774951 (GRCh38)
Gene constraint: LOEUF 0.446 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 79.28 · 130 PDB

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

Disease context

renal cell carcinoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome

Similar variants

MET p.Pro1033Arg Uncertain significance ★★ ⚠ same residue
MET p.Pro1033Ala Uncertain significance ★ ⚠ same residue
MET p.Pro1033Ser Uncertain significance ★ ⚠ same residue
MET p.Pro1033Leu Uncertain significance ★ ⚠ same residue
MET p.His1094Arg Pathogenic/Likely pathogenic ★★ ⚠ same condition
MET p.Met1131Thr Pathogenic/Likely pathogenic ★★ same condition
MET p.Val1092Ile Pathogenic/Likely pathogenic ★★ same condition
MET p.Val1220Ile 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/met-p-pro1033 (accessed [today's date]).

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