Is SDHB p.Ile263= (c.789T>C) pathogenic?

SDHB p.Ile263= (c.789T>C) is classified Benign/Likely benign in SDHB (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-03-13). Very rare (popmax 0.00167%, amr); Associated with pheochromocytoma/paraganglioma syndrome 4.

What condition is associated with SDHB p.Ile263= (c.789T>C)?

SDHB p.Ile263= (c.789T>C) is associated with pheochromocytoma/paraganglioma syndrome 4, pheochromocytoma, gastrointestinal stromal tumor (ClinVar).

How common is SDHB p.Ile263= (c.789T>C) in the general population?

SDHB p.Ile263= (c.789T>C) is very rare (popmax 0.00167%, amr) (gnomAD).

SDHB p.Ile263=

c.789T>C · rs1395418494 · VCV827319

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

pheochromocytoma/paraganglioma syndrome 4

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 0.56	GERP 1.2, phastCons 0.87
Overall
CADD	6.785	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/59,994 alleles

Overall 6.85e-05% 1/1,460,280 alleles · very rare

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: SDHB
Protein: p.Ile263=
Coding: c.789T>C
MANE Select: NM_003000
dbSNP: rs1395418494
Type: single nucleotide variant
Location: chr1:17018935 (GRCh38)
Gene constraint: LOEUF 0.741 · pLI 0.03 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 92.14 · 6 PDB
Residue 263: an α-helix

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

Disease context

pheochromocytoma/paraganglioma syndrome 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: pheochromocytoma gastrointestinal stromal tumor hereditary neoplastic syndrome

Similar variants

SDHB p.Ile263Val Uncertain significance ★★ ⚠ same residue
SDHB p.Ile263Thr Uncertain significance ★ ⚠ same residue
SDHB p.Ile263fs Likely pathogenic ★★ same residue
SDHB c.200+1G>A Pathogenic ★★ same condition
SDHB c.200+1G>C Pathogenic/Likely pathogenic ★★ same condition
SDHB c.200+5G>T Likely pathogenic ★★ same condition
SDHB c.201-1G>C Pathogenic/Likely pathogenic ★★ same condition
SDHB c.201-2A>C 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/sdhb-p-ile263 (accessed [today's date]).

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