Is SUFU p.Arg299fs (c.893_894insTGCCCCG) pathogenic?

SUFU p.Arg299fs (c.893894insTGCCCCG) is classified Pathogenic in SUFU (ClinVar, Single submitter, 1 submitter; last evaluated 2020-04-07). No gnomAD frequency available for this variant; Associated with nevoid basal cell carcinoma syndrome.

What condition is associated with SUFU p.Arg299fs (c.893_894insTGCCCCG)?

SUFU p.Arg299fs (c.893_894insTGCCCCG) is associated with nevoid basal cell carcinoma syndrome, medulloblastoma (ClinVar).

How common is SUFU p.Arg299fs (c.893_894insTGCCCCG) in the general population?

SUFU p.Arg299fs (c.893_894insTGCCCCG) is no gnomAD frequency available for this variant (gnomAD).

SUFU p.Arg299fs

c.893_894insTGCCCCG · rs2135882232 · VCV1075819

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

nevoid basal cell carcinoma syndrome

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 7 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.9, 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.Arg299fs
Coding: c.893_894insTGCCCCG
MANE Select: NM_016169
dbSNP: rs2135882232
Type: Insertion
Location: chr10:102597270 (GRCh38)
Gene constraint: LOEUF 0.214 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 82.95 · 10 PDB
Residue 299: the 'disordered' region; a UniProt-annotated variant site (sequence variant)

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

Disease context

nevoid basal cell carcinoma syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: medulloblastoma

Similar variants

SUFU p.Arg299Ter Pathogenic ★★ same residue
SUFU p.Arg299Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
SUFU p.Arg299Gly Uncertain significance ★ same residue
SUFU p.Leu300fs Pathogenic ★★ same condition
SUFU c.1158-10_1158-9insT Likely benign ★ same condition
SUFU c.1158-8_1158-7insCTG Likely benign ★ same condition
SUFU c.1022+1G>A Pathogenic ★★ same condition
SUFU c.1023-2A>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/sufu-p-arg299fs (accessed [today's date]).

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