Is SI p.Gln90fs (c.267del) pathogenic?

SI p.Gln90fs (c.267del) is classified Pathogenic in SI (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-03). Absent from gnomAD.

How common is SI p.Gln90fs (c.267del) in the general population?

SI p.Gln90fs (c.267del) is absent from gnomAD (gnomAD).

SI p.Gln90fs

c.267del · rs2473438329 · VCV2826123

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
NMD	predicted	premature termination codon in exon 4 of 48
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.024	GERP -2.7

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.Gln90fs
Coding: c.267del
MANE Select: NM_001041
dbSNP: rs2473438329
Type: Deletion
Location: chr3:165069184 (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 90: a disulfide bond; the p-type 1 domain; an α-helix

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

Similar variants

SI p.Gln90Arg Uncertain significance ★ ⚠ same residue
SI p.Asn1403fs Pathogenic/Likely pathogenic ★★ same type
SI p.Gln278fs Pathogenic/Likely pathogenic ★★ same type
SI p.Leu1062_Tyr1063insTer Pathogenic/Likely pathogenic ★★ same type
SI p.Phe295_Leu296insTer Pathogenic/Likely pathogenic ★★ same type
SI p.Val342fs Pathogenic/Likely pathogenic ★★ same type
SI c.2737-11del Benign/Likely benign ★★ same type
SI c.2737-12_2737-11del Benign/Likely benign ★★ 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/si-p-gln90fs (accessed [today's date]).

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