Is KDR p.Leu902Gln (c.2705T>A) pathogenic?

KDR p.Leu902Gln (c.2705T>A) is classified Uncertain significance in KDR (ClinVar, No assertion criteria, 1 submitter; last evaluated 2015-01-24). AlphaMissense: likely pathogenic (0.9285); Absent from gnomAD v4.1; Associated with colon carcinoma.

What condition is associated with KDR p.Leu902Gln (c.2705T>A)?

KDR p.Leu902Gln (c.2705T>A) is associated with colon carcinoma (ClinVar).

How common is KDR p.Leu902Gln (c.2705T>A) in the general population?

KDR p.Leu902Gln (c.2705T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about KDR p.Leu902Gln (c.2705T>A)?

AlphaMissense predicts likely pathogenic (score 0.9285) — an in-silico prediction, not a clinical call.

KDR p.Leu902Gln

c.2705T>A · rs794729678 · VCV204328

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9285 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

colon carcinoma

Computational evidence

Protein change
AlphaMissense	0.9285	likely pathogenic
REVEL	0.909	moderately pathogenic-leaning
SaProt	LLR -14.37	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.8, phastCons 1
Regional constraint	o/e 0.73	unconstrained · MANE · 5,468 bp · p 9.5e-05 · regional, not allelic
Overall
CADD	29.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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: KDR
Protein: p.Leu902Gln
Coding: c.2705T>A
MANE Select: NM_002253
dbSNP: rs794729678
Type: single nucleotide variant
Location: chr4:55096252 (GRCh38)
Gene constraint: LOEUF 0.328 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 71.67 · 54 PDB
Residue 902: the protein kinase domain; a β-strand

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

Disease context

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

Similar variants

KDR c.2509+20T>A Uncertain significance same condition
KDR c.2615-23C>T Uncertain significance same condition
KDR c.3405-4C>T Uncertain significance same condition
KDR p.Ala866= Uncertain significance same condition
KDR p.Glu1155= Uncertain significance same condition
KDR p.Gly794Arg Uncertain significance ⚠ same condition
KDR p.Ile892= Uncertain significance same condition
KDR p.Leu1163Phe Uncertain significance ⚠ 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/kdr-p-leu902gln (accessed [today's date]).

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