Is ILF3 p.Ser892Ile (c.2675G>T) pathogenic?

ILF3 p.Ser892Ile (c.2675G>T) is classified Uncertain significance in ILF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-15). AlphaMissense: likely pathogenic (0.6931); Absent from gnomAD v4.1.

How common is ILF3 p.Ser892Ile (c.2675G>T) in the general population?

ILF3 p.Ser892Ile (c.2675G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ILF3 p.Ser892Ile (c.2675G>T)?

AlphaMissense predicts likely pathogenic (score 0.6931) — an in-silico prediction, not a clinical call.

ILF3 p.Ser892Ile

c.2675G>T · VCV4275250

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6931 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.6931	likely pathogenic
REVEL	0.126	moderately benign-leaning
SaProt	LLR -9.87	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 10	GERP 1.7, phastCons 1
Overall
CADD	24.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM S888I vs ClinVar S892I) — verify the residue.

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: ILF3
Protein: p.Ser892Ile
Coding: c.2675G>T
MANE Select: NM_017620
Type: single nucleotide variant
Location: chr19:10689290 (GRCh38)
Gene constraint: LOEUF 0.309 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 67.74 · 4 PDB
Residue 888 UniProt numbering: the 'interaction with prmt1' region; the 'disordered' region

Full ILF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ILF3 p.Arg655= Benign ★★ same type
ILF3 p.Ala123Thr Uncertain significance ★ ⚠ same type
ILF3 p.Ala268Val Uncertain significance ★ ⚠ same type
ILF3 p.Ala397Ser Uncertain significance ★ ⚠ same type
ILF3 p.Ala488Thr Uncertain significance ★ ⚠ same type
ILF3 p.Ala494Val Uncertain significance ★ ⚠ same type
ILF3 p.Ala507Val Uncertain significance ★ ⚠ same type
ILF3 p.Ala515Val Uncertain significance ★ ⚠ 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/ilf3-p-ser892ile (accessed [today's date]).

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