Is LRIG2 p.Ser697fs (c.2088del) pathogenic?

LRIG2 p.Ser697fs (c.2088del) is classified Pathogenic in LRIG2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2013-02-07). No gnomAD frequency available for this variant; Associated with urofacial syndrome 2.

What condition is associated with LRIG2 p.Ser697fs (c.2088del)?

LRIG2 p.Ser697fs (c.2088del) is associated with urofacial syndrome 2 (ClinVar).

How common is LRIG2 p.Ser697fs (c.2088del) in the general population?

LRIG2 p.Ser697fs (c.2088del) is no gnomAD frequency available for this variant (gnomAD).

LRIG2 p.Ser697fs

c.2088del · rs587776947 · VCV40208

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

urofacial syndrome 2

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 15 of 18
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.13	GERP -2.3, phastCons 0.12

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: LRIG2
Protein: p.Ser697fs
Coding: c.2088del
MANE Select: NM_014813
dbSNP: rs587776947
Type: Deletion
Location: chr1:113114432 (GRCh38)
Gene constraint: LOEUF 0.95 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.87
Residue 697: the ig-like c2-type 3 domain

Full LRIG2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

urofacial syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LRIG2 p.Glu926fs Likely pathogenic ★ same condition
LRIG2 p.Ser175fs Likely pathogenic ★ same condition
LRIG2 p.Glu410fs Pathogenic same condition
LRIG2 p.Arg86Trp Uncertain significance ★★ ⚠ same condition
LRIG2 p.Glu11Ter Uncertain significance ★★ same condition
LRIG2 c.2531-22G>A Benign ★★ same condition
LRIG2 p.Thr708= Benign ★★ same condition
LRIG2 c.1799-2_1799-1delAG 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/lrig2-p-ser697fs (accessed [today's date]).

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