Is KDR p.Arg787Gln (c.2360G>A) pathogenic?

KDR p.Arg787Gln (c.2360G>A) is classified Uncertain significance in KDR (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: likely benign (0.1967); Ultra-rare (popmax 0.0178%, eas); Associated with prostate cancer.

What condition is associated with KDR p.Arg787Gln (c.2360G>A)?

KDR p.Arg787Gln (c.2360G>A) is associated with prostate cancer (ClinVar).

How common is KDR p.Arg787Gln (c.2360G>A) in the general population?

KDR p.Arg787Gln (c.2360G>A) is ultra-rare (popmax 0.0178%, eas) (gnomAD).

What do computational predictors say about KDR p.Arg787Gln (c.2360G>A)?

AlphaMissense predicts likely benign (score 0.1967) — an in-silico prediction, not a clinical call.

KDR p.Arg787Gln

c.2360G>A · rs193921127 · VCV161593

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1967 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0178%, eas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

prostate cancer

Computational evidence

Protein change
AlphaMissense	0.1967	likely benign
REVEL	0.622	indeterminate
SaProt	LLR -8.33	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.8, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 3,772 bp · p 0.5 · regional, not allelic
Overall
CADD	30.0	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

Grpmax group 0.0178% East Asian · 8/44,852 alleles

Filtering AF 0.00884% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00641%

Overall 0.00174% 28/1,611,840 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0178%	5,607
African / African-American	0.00267%	37,395
Admixed American	0.00167%	59,936
Remaining individualsnot grpmax-eligible	0.0016%	62,386
European (non-Finnish)	0.00136%	73,642

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: KDR
Protein: p.Arg787Gln
Coding: c.2360G>A
MANE Select: NM_002253
dbSNP: rs193921127
Type: single nucleotide variant
Location: chr4:55098710 (GRCh38)
Gene constraint: LOEUF 0.328 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 71.67 · 54 PDB
Residue 787: an α-helix

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

Disease context

prostate cancer — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KDR p.Ala379Val Uncertain significance ★★ ⚠ same type
KDR p.Ala757Gly Uncertain significance ★★ ⚠ same type
KDR p.Asp832His Uncertain significance ★★ ⚠ same type
KDR p.Val416Ala Uncertain significance ★★ ⚠ same type
KDR p.Ala1030= Benign ★★ same type
KDR p.Ala532= Benign ★★ same type
KDR p.Arg842His Likely benign ★★ ⚠ same type
KDR p.Cys482Arg Likely benign ★★ same type

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-arg787gln (accessed [today's date]).

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