Is SDHB p.Val5= (c.15C>G) pathogenic?

SDHB p.Val5= (c.15C>G) is classified Likely benign in SDHB (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-09-14). Very rare (popmax 6.86e-05%); Associated with pheochromocytoma.

What condition is associated with SDHB p.Val5= (c.15C>G)?

SDHB p.Val5= (c.15C>G) is associated with pheochromocytoma, pheochromocytoma/paraganglioma syndrome 4, gastrointestinal stromal tumor (ClinVar).

How common is SDHB p.Val5= (c.15C>G) in the general population?

SDHB p.Val5= (c.15C>G) is very rare (popmax 6.86e-05%) (gnomAD).

SDHB p.Val5=

c.15C>G · rs1182998682 · VCV1132119

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 6.86e-05%)

Conditions

pheochromocytoma

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 0.14	GERP -2.9, phastCons 0.007
Overall
CADD	7.538	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.86e-05%

Overall 6.86e-05% 1/1,458,294 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.Val5=
Coding: c.15C>G
MANE Select: NM_003000
dbSNP: rs1182998682
Type: single nucleotide variant
Location: chr1:17054005 (GRCh38)
Gene constraint: LOEUF 0.741 · pLI 0.03 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 92.14 · 6 PDB

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

Disease context

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

Also linked: pheochromocytoma/paraganglioma syndrome 4 gastrointestinal stromal tumor hereditary neoplastic syndrome

Similar variants

SDHB p.Val5Ala Uncertain significance ★★ ⚠ same residue
SDHB p.Val5Gly Uncertain significance ★★ ⚠ same residue
SDHB p.Val5Leu Uncertain significance ★ ⚠ same residue
SDHB p.Val5Phe Uncertain significance ★ ⚠ same residue
SDHB p.Val5_Ala6= Benign ★ 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

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-val5 (accessed [today's date]).

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