Is LINS1 p.Arg102Gln (c.305_306delinsAA) pathogenic?

LINS1 p.Arg102Gln (c.305306delinsAA) is classified Uncertain significance in LINS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-27). No gnomAD frequency available for this variant; Associated with intellectual disability, autosomal recessive 27.

What condition is associated with LINS1 p.Arg102Gln (c.305_306delinsAA)?

LINS1 p.Arg102Gln (c.305_306delinsAA) is associated with intellectual disability, autosomal recessive 27 (ClinVar).

How common is LINS1 p.Arg102Gln (c.305_306delinsAA) in the general population?

LINS1 p.Arg102Gln (c.305_306delinsAA) is no gnomAD frequency available for this variant (gnomAD).

LINS1 p.Arg102Gln

c.305_306delinsAA · rs2038477427 · VCV1031763

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

intellectual disability, autosomal recessive 27

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.71	GERP -5.4
Regional constraint	o/e 1.08	unconstrained · MANE · 12 kb · p 0.017 · regional, not allelic

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: LINS1
Protein: p.Arg102Gln
Coding: c.305_306delinsAA
MANE Select: NM_001040616
dbSNP: rs2038477427
Type: Indel
Location: chr15:100580537 (GRCh38)
Gene constraint: LOEUF 0.867 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.44

Full LINS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability, autosomal recessive 27 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LINS1 p.Arg102fs Conflicting classifications of pathogenicity ★ same residue
LINS1 p.Glu641fs Likely pathogenic ★★ same condition
LINS1 p.Gly558fs Pathogenic ★★ same condition
LINS1 p.His328fs Pathogenic ★★ same condition
LINS1 p.Leu393Ter Pathogenic/Likely pathogenic ★★ same condition
LINS1 p.Ala338Val Uncertain significance ★★ ⚠ same condition
LINS1 p.Asp221Asn Uncertain significance ★★ ⚠ same condition
LINS1 p.Ile494Thr Uncertain significance ★★ ⚠ 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/lins1-p-arg102gln (accessed [today's date]).

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