Is SBF1 p.Pro1106fs (c.3317del) pathogenic?

SBF1 p.Pro1106fs (c.3317del) is classified Pathogenic in SBF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-19). No gnomAD frequency available for this variant.

How common is SBF1 p.Pro1106fs (c.3317del) in the general population?

SBF1 p.Pro1106fs (c.3317del) is no gnomAD frequency available for this variant (gnomAD).

SBF1 p.Pro1106fs

c.3317del · rs2067440192 · VCV1952532

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

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 LoF-intolerant gene
NMD	predicted	premature termination codon in exon 26 of 41
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -11	GERP -3.9

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: SBF1
Protein: p.Pro1106fs
Coding: c.3317del
MANE Select: NM_002972
dbSNP: rs2067440192
Type: Deletion
Location: chr22:50460126 (GRCh38)
Gene constraint: LOEUF 0.381 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 74.72
Residue 1106: the 'disordered' region

Full SBF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SBF1 p.Pro1106Leu Uncertain significance ★★ ⚠ same residue
SBF1 p.Pro1106= Likely benign ★★ same residue
SBF1 p.Asp719fs Pathogenic/Likely pathogenic ★★ same type
SBF1 c.141+10_141+12del Benign ★★ same type
SBF1 c.2396+7_2396+18del Benign ★★ same type
SBF1 c.3826+17del Likely benign ★★ same type
SBF1 p.Arg1607fs Pathogenic ★ same type
SBF1 p.Phe1150fs Pathogenic ★ same type

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/sbf1-p-pro1106fs (accessed [today's date]).

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