Is KDR p.Ser1311= (c.3933C>T) pathogenic?

KDR p.Ser1311= (c.3933C>T) is classified Likely benign in KDR (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-25). Ultra-rare (popmax 0.0604%, sas); Associated with KDR-related disorder.

What condition is associated with KDR p.Ser1311= (c.3933C>T)?

KDR p.Ser1311= (c.3933C>T) is associated with KDR-related disorder (ClinVar).

How common is KDR p.Ser1311= (c.3933C>T) in the general population?

KDR p.Ser1311= (c.3933C>T) is ultra-rare (popmax 0.0604%, sas) (gnomAD).

KDR p.Ser1311=

c.3933C>T · rs774371518 · VCV3058351

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0604%, sas)

Conditions

KDR-related disorder

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 -13	GERP -5.5
Overall
CADD	0.079	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0604% South Asian · 55/91,078 alleles

Filtering AF 0.0476% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.043%

Overall 0.00527% 85/1,614,142 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0604%	1,656
Middle Eastern	0.0166%	6,032
Remaining individualsnot grpmax-eligible	0.0064%	15,626
Admixed American	0.00333%	30,016
European (non-Finnish)	0.00186%	53,637
African / African-American	0.00133%	75,034

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.Ser1311=
Coding: c.3933C>T
MANE Select: NM_002253
dbSNP: rs774371518
Type: single nucleotide variant
Location: chr4:55080079 (GRCh38)
Gene constraint: LOEUF 0.328 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 71.67 · 54 PDB
Residue 1311: the 'disordered' region

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

Disease context

KDR-related disorder

Similar variants

KDR p.Gly1092Arg Uncertain significance ⚠ same condition
KDR c.1537-6G>A Likely benign same condition
KDR c.3510+10C>T Likely benign same condition
KDR c.-1G>T Benign same condition
KDR p.Gln472His Benign same condition
KDR p.Gly1283= Likely benign same condition
KDR p.Ile1330Leu Benign same condition
KDR p.Lys941= Likely benign 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-ser1311 (accessed [today's date]).

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