Is SUFU p.Arg239= (c.715C>A) pathogenic?

SUFU p.Arg239= (c.715C>A) is classified Likely benign in SUFU (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-08-31). Very rare (popmax 0.00934%, afr); Associated with medulloblastoma.

What condition is associated with SUFU p.Arg239= (c.715C>A)?

SUFU p.Arg239= (c.715C>A) is associated with medulloblastoma, nevoid basal cell carcinoma syndrome, hereditary neoplastic syndrome (ClinVar).

How common is SUFU p.Arg239= (c.715C>A) in the general population?

SUFU p.Arg239= (c.715C>A) is very rare (popmax 0.00934%, afr) (gnomAD).

How is Medulloblastoma inherited?

Typically Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

SUFU p.Arg239=

c.715C>A · rs369465986 · VCV453976

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00934%, afr)

Conditions

medulloblastoma

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 · C>G here scores Δ0.52 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.1	GERP 1.8, phastCons 1
Overall
CADD	9.558	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00934% African / African-American · 7/74,908 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00309%

Overall 0.00273% 44/1,613,986 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00934%	10,701
European (non-Finnish)	0.00314%	31,892

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: SUFU
Protein: p.Arg239=
Coding: c.715C>A
MANE Select: NM_016169
dbSNP: rs369465986
Type: single nucleotide variant
Location: chr10:102594024 (GRCh38)
Gene constraint: LOEUF 0.214 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 82.95 · 10 PDB

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

Disease context

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

Also linked: nevoid basal cell carcinoma syndrome hereditary neoplastic syndrome

For Medulloblastoma (Orphanet):

Inheritance: Not applicable
Onset: All ages
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

SUFU p.Arg239Gln Uncertain significance ★★ ⚠ same residue
SUFU p.Arg239Gly Uncertain significance ★ ⚠ same residue
SUFU p.Arg239Trp Uncertain significance ★ ⚠ same residue
SUFU c.1022+1G>A Pathogenic ★★ same condition
SUFU c.1023-2A>T Likely pathogenic ★★ same condition
SUFU c.683+1G>A Likely pathogenic ★★ same condition
SUFU c.684-2A>G Likely pathogenic ★★ same condition
SUFU p.Arg146Ter 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/sufu-p-arg239 (accessed [today's date]).

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