Is SUOX p.Pro200= (c.600T>C) pathogenic?

SUOX p.Pro200= (c.600T>C) is classified Likely benign in SUOX (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-09). Very rare (popmax 0.0061%, nfe); Associated with isolated sulfite oxidase deficiency.

What condition is associated with SUOX p.Pro200= (c.600T>C)?

SUOX p.Pro200= (c.600T>C) is associated with isolated sulfite oxidase deficiency (ClinVar).

How common is SUOX p.Pro200= (c.600T>C) in the general population?

SUOX p.Pro200= (c.600T>C) is very rare (popmax 0.0061%, nfe) (gnomAD).

SUOX p.Pro200=

Q: How is Encephalopathy due to sulfite oxidase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.600T>C · rs373848904 · VCV1111414

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0061%, nfe)

Conditions

isolated sulfite oxidase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.7	GERP 1.3, phastCons 0.93
Overall
CADD	9.542	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0061% European (non-Finnish) · 72/1,180,010 alleles

Filtering AF 0.00495% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00455%

Overall 0.00446% 72/1,614,130 alleles · very rare exomes 72/1,461,882 · genomes 0/152,248 · joint denominator

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: SUOX
Protein: p.Pro200=
Coding: c.600T>C
MANE Select: NM_001032386
dbSNP: rs373848904
Type: single nucleotide variant
Location: chr12:56003989 (GRCh38)
Gene constraint: LOEUF 1.128 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.99 · 1 PDB
Residue 200: the 'moco domain' region

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

Disease context

isolated sulfite oxidase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Encephalopathy due to sulfite oxidase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Antenatal, Infancy, Neonatal

Similar variants

SUOX p.Pro200Leu Likely pathogenic ★ ⚠ same residue
SUOX p.Pro200Ala Uncertain significance ★ ⚠ same residue
SUOX p.Pro200fs Pathogenic ★ same residue
SUOX c.228+1G>A Pathogenic/Likely pathogenic ★★ same condition
SUOX c.51-2A>C Likely pathogenic ★★ same condition
SUOX p.Arg217Gln Pathogenic/Likely pathogenic ★★ same condition
SUOX p.Arg366His Pathogenic/Likely pathogenic ★★ same condition
SUOX p.Arg459Gln 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/suox-p-pro200 (accessed [today's date]).

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