Is SI p.Gln265fs (c.793del) pathogenic?

SI p.Gln265fs (c.793del) is classified Pathogenic in SI (ClinVar, Single submitter, 1 submitter; last evaluated 2021-06-30). Absent from gnomAD; Associated with congenital sucrase-isomaltase deficiency.

What condition is associated with SI p.Gln265fs (c.793del)?

SI p.Gln265fs (c.793del) is associated with congenital sucrase-isomaltase deficiency (ClinVar).

How common is SI p.Gln265fs (c.793del) in the general population?

SI p.Gln265fs (c.793del) is absent from gnomAD (gnomAD).

How is Congenital sucrase-isomaltase deficiency inherited?

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

SI p.Gln265fs

c.793del · rs1714177959 · VCV1179179

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

congenital sucrase-isomaltase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 7 of 48
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.2	GERP 0.65, 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: SI
Protein: p.Gln265fs
Coding: c.793del
MANE Select: NM_001041
dbSNP: rs1714177959
Type: Deletion
Location: chr3:165065275 (GRCh38)
Gene constraint: LOEUF 1.009 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.86 · 2 PDB
Residue 265: the 'isomaltase' region

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

Disease context

congenital sucrase-isomaltase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Congenital sucrase-isomaltase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

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SI p.Gln278fs Pathogenic/Likely pathogenic ★★ same condition
SI p.Leu1062_Tyr1063insTer Pathogenic/Likely pathogenic ★★ same condition
SI p.Val342fs Pathogenic/Likely pathogenic ★★ same condition
SI c.2737-11del Benign/Likely benign ★★ same condition
SI c.2737-12_2737-11del Benign/Likely benign ★★ same condition
SI c.2737-17_2737-11del Likely benign ★★ same condition
SI c.3634-5del Benign/Likely benign ★★ 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/si-p-gln265fs (accessed [today's date]).

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