Is ILF3 p.Asp804Ala (c.2411A>C) pathogenic?

ILF3 p.Asp804Ala (c.2411A>C) is classified Uncertain significance in ILF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-09). AlphaMissense: ambiguous (0.4807); Very rare (popmax 0.00161%, nfe).

How common is ILF3 p.Asp804Ala (c.2411A>C) in the general population?

ILF3 p.Asp804Ala (c.2411A>C) is very rare (popmax 0.00161%, nfe) (gnomAD).

What do computational predictors say about ILF3 p.Asp804Ala (c.2411A>C)?

AlphaMissense predicts ambiguous (score 0.4807) — an in-silico prediction, not a clinical call.

ILF3 p.Asp804Ala

c.2411A>C · VCV4678750

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4807 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00161%, nfe)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.4807	ambiguous
REVEL	0.198	benign-leaning
SaProt	LLR -5.93	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.7, phastCons 1
Overall
CADD	24.7	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 D800A vs ClinVar D804A) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00161% European (non-Finnish) · 19/1,179,824 alleles

Filtering AF 0.00103% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00083%

Overall 0.0013% 21/1,612,908 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00161%	62,096
Remaining individualsnot grpmax-eligible	0.0016%	62,470
African / African-American	0.00134%	74,892

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ILF3
Protein: p.Asp804Ala
Coding: c.2411A>C
MANE Select: NM_017620
Type: single nucleotide variant
Location: chr19:10687685 (GRCh38)
Gene constraint: LOEUF 0.309 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 67.74 · 4 PDB
Residue 804: 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-asp804ala (accessed [today's date]).

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