Is SUFU p.Pro49fs (c.143dup) pathogenic?

SUFU p.Pro49fs (c.143dup) is classified Pathogenic in SUFU (ClinVar, No assertion criteria, 1 submitter; last evaluated 2002-07-01). No gnomAD frequency available for this variant; Associated with medulloblastoma.

What condition is associated with SUFU p.Pro49fs (c.143dup)?

SUFU p.Pro49fs (c.143dup) is associated with medulloblastoma (ClinVar).

How common is SUFU p.Pro49fs (c.143dup) in the general population?

SUFU p.Pro49fs (c.143dup) is no gnomAD frequency available for this variant (gnomAD).

How is Medulloblastoma inherited?

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

SUFU p.Pro49fs

c.143dup · rs1589970134 · VCV3570

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

medulloblastoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 1 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.5	GERP 1.6, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SUFU
Protein: p.Pro49fs
Coding: c.143dup
MANE Select: NM_016169
dbSNP: rs1589970134
Type: Duplication
Location: chr10:102504294 (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

For Medulloblastoma (Orphanet):

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

Similar variants

SUFU p.Pro49Leu Uncertain significance ★★ ⚠ same residue
SUFU p.Pro49Ala Uncertain significance ★ ⚠ same residue
SUFU p.Thr196fs Pathogenic ★★ same condition
SUFU p.Leu312_Arg313insLeu Uncertain significance ★★ same condition
SUFU p.Arg42fs Pathogenic ★ same condition
SUFU p.Cys273fs Pathogenic ★ same condition
SUFU p.Gly193fs Pathogenic ★ same condition
SUFU p.Phe417fs 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-pro49fs (accessed [today's date]).

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