Is LINS1 p.His432= (c.1296C>T) pathogenic?

LINS1 p.His432= (c.1296C>T) is classified Likely benign in LINS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-19). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with LINS1 p.His432= (c.1296C>T)?

LINS1 p.His432= (c.1296C>T) is associated with Inborn genetic diseases (ClinVar).

How common is LINS1 p.His432= (c.1296C>T) in the general population?

LINS1 p.His432= (c.1296C>T) is absent from gnomAD v4.1 (gnomAD).

LINS1 p.His432=

c.1296C>T · rs2505351601 · VCV1800396

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.99 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.058	GERP -4.5
Overall
CADD	7.165	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: LINS1
Protein: p.His432=
Coding: c.1296C>T
MANE Select: NM_001040616
dbSNP: rs2505351601
Type: single nucleotide variant
Location: chr15:100571992 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LINS1 c.1394+4A>G Uncertain significance ★★ same condition
LINS1 p.Ala338Val Uncertain significance ★★ ⚠ same condition
LINS1 p.Asn433Ser Uncertain significance ★★ ⚠ same condition
LINS1 p.Asp630Asn Uncertain significance ★★ ⚠ same condition
LINS1 p.Ile494Thr Uncertain significance ★★ ⚠ same condition
LINS1 p.Leu757Ter Uncertain significance ★★ same condition
LINS1 p.Met449Ile Uncertain significance ★★ ⚠ same condition
LINS1 p.Ala331Val 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/lins1-p-his432 (accessed [today's date]).

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