Is SDHAF2 p.Pro112= (c.336T>C) pathogenic?

SDHAF2 p.Pro112= (c.336T>C) is classified Likely benign in SDHAF2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-10). Very rare (popmax 0.00133%, afr); Associated with hereditary pheochromocytoma-paraganglioma.

What condition is associated with SDHAF2 p.Pro112= (c.336T>C)?

SDHAF2 p.Pro112= (c.336T>C) is associated with hereditary pheochromocytoma-paraganglioma, hereditary neoplastic syndrome (ClinVar).

How common is SDHAF2 p.Pro112= (c.336T>C) in the general population?

SDHAF2 p.Pro112= (c.336T>C) is very rare (popmax 0.00133%, afr) (gnomAD).

How is Hereditary pheochromocytoma-paraganglioma inherited?

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

SDHAF2 p.Pro112=

c.336T>C · VCV4808179

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Conditions

hereditary pheochromocytoma-paraganglioma

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 · T>A here scores Δ0.54 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.21	GERP -3.5, phastCons 0.35
Overall
CADD	14.49	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/75,038 alleles

Overall 6.2e-05% 1/1,614,036 alleles · very rare exomes 1/1,461,740 · genomes 0/152,296 · 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: SDHAF2
Protein: p.Pro112=
Coding: c.336T>C
MANE Select: NM_017841
Type: single nucleotide variant
Location: chr11:61438079 (GRCh38)
Gene constraint: LOEUF 1.608 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 84.06 · 2 PDB

Full SDHAF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Also linked: hereditary neoplastic syndrome

For Hereditary pheochromocytoma-paraganglioma (Orphanet):

Inheritance: Autosomal dominant
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Worldwide)

Similar variants

SDHAF2 p.Pro112Thr Uncertain significance ★★ ⚠ same residue
SDHAF2 p.Pro112Leu Uncertain significance ★ ⚠ same residue
SDHAF2 p.Pro112Ser Uncertain significance ★ ⚠ same residue
SDHAF2 c.260+1G>A Likely pathogenic ★★ same condition
SDHAF2 c.261-2A>G Likely pathogenic ★★ same condition
SDHAF2 c.261-2A>T Likely pathogenic ★★ same condition
SDHAF2 c.37-1G>C Pathogenic/Likely pathogenic ★★ same condition
SDHAF2 c.37-2A>G 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/sdhaf2-p-pro112 (accessed [today's date]).

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