Is ILF3 p.Pro641His (c.1922C>A) pathogenic?

ILF3 p.Pro641His (c.1922C>A) is classified Uncertain significance in ILF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-24). AlphaMissense: likely benign (0.2042); Ultra-rare (popmax 0.01%, amr).

How common is ILF3 p.Pro641His (c.1922C>A) in the general population?

ILF3 p.Pro641His (c.1922C>A) is ultra-rare (popmax 0.01%, amr) (gnomAD).

What do computational predictors say about ILF3 p.Pro641His (c.1922C>A)?

AlphaMissense predicts likely benign (score 0.2042) — an in-silico prediction, not a clinical call.

ILF3 p.Pro641His

c.1922C>A · VCV4038507

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2042 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.01%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2042	likely benign
REVEL	0.064	moderately benign-leaning
SaProt	LLR -7.66	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 0.65, phastCons 1
Overall
CADD	24.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM P637H vs ClinVar P641H) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.01% Admixed American · 6/59,992 alleles

Filtering AF 0.00428% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00295%

Overall 0.000496% 8/1,613,924 alleles · ultra-rare exomes 6/1,461,758 · genomes 2/152,166 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.01%	9,999
Remaining individualsnot grpmax-eligible	0.0032%	31,237

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.Pro641His
Coding: c.1922C>A
MANE Select: NM_017620
Type: single nucleotide variant
Location: chr19:10683694 (GRCh38)
Gene constraint: LOEUF 0.309 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 67.74 · 4 PDB
Residue 637 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-pro641his (accessed [today's date]).

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