Is SDHB p.Ile79= (c.237T>A) pathogenic?

SDHB p.Ile79= (c.237T>A) is classified Likely benign in SDHB (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-13). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with SDHB p.Ile79= (c.237T>A)?

SDHB p.Ile79= (c.237T>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is SDHB p.Ile79= (c.237T>A) in the general population?

SDHB p.Ile79= (c.237T>A) is absent from gnomAD v4.1 (gnomAD).

SDHB p.Ile79=

c.237T>A · VCV3316898

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

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 1.7	GERP -1.2, phastCons 1
Overall
CADD	9.36	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SDHB
Protein: p.Ile79=
Coding: c.237T>A
MANE Select: NM_003000
Type: single nucleotide variant
Location: chr1:17033109 (GRCh38)
Gene constraint: LOEUF 0.741 · pLI 0.03 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 92.14 · 6 PDB
Residue 79: the 2fe-2s ferredoxin-type domain; an α-helix

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SDHB p.Ile79Met Uncertain significance ★★ ⚠ same residue
SDHB p.Ile79Phe Uncertain significance ★★ ⚠ same residue
SDHB p.Ile79Thr Uncertain significance ★ ⚠ same residue
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
SDHB c.286+1G>A 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-ile79 (accessed [today's date]).

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