Is DPYD p.Ser550= (c.1650C>T) pathogenic?

DPYD p.Ser550= (c.1650C>T) is classified Likely benign in DPYD (ClinVar, Single submitter, 1 submitter; last evaluated 2019-06-29). Very rare (popmax 0.00329%, sas); Associated with Inborn genetic diseases.

What condition is associated with DPYD p.Ser550= (c.1650C>T)?

DPYD p.Ser550= (c.1650C>T) is associated with Inborn genetic diseases (ClinVar).

How common is DPYD p.Ser550= (c.1650C>T) in the general population?

DPYD p.Ser550= (c.1650C>T) is very rare (popmax 0.00329%, sas) (gnomAD).

DPYD p.Ser550=

c.1650C>T · rs149101842 · VCV1777250

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00329%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.46 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.51	GERP -4.3
Overall
CADD	7.979	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00329% South Asian · 3/91,056 alleles

Filtering AF 0.000878% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000718%

Overall 0.00143% 23/1,612,846 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00329%	30,352
Remaining individualsnot grpmax-eligible	0.0032%	31,215
East Asian	0.00223%	44,838
European (non-Finnish)	0.00144%	69,369

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: DPYD
Protein: p.Ser550=
Coding: c.1650C>T
MANE Select: NM_000110
dbSNP: rs149101842
Type: single nucleotide variant
Location: chr1:97515816 (GRCh38)
Gene constraint: LOEUF 1.09 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 96.23
Residue 550: a binding site

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DPYD p.Ala513Val Uncertain significance ★★ ⚠ same condition
DPYD p.Ala664Ser Uncertain significance ★★ ⚠ same condition
DPYD p.Arg332Gln Uncertain significance ★★ ⚠ same condition
DPYD p.Arg410Gln Uncertain significance ★★ ⚠ same condition
DPYD p.Arg692Gln Uncertain significance ★★ ⚠ same condition
DPYD p.Gln508= Uncertain significance ★★ same condition
DPYD p.Glu13Lys Uncertain significance ★★ ⚠ same condition
DPYD p.Glu950Lys 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/dpyd-p-ser550 (accessed [today's date]).

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