Curation FRA2A AFF3

Two probands with intellectual disability underwent PacBio HiFi trio sequencing, confirming heterozygous expanded AFF3 GCC alleles (157 and 822 copies) inherited from a carrier parent with methylation and size changes on transmission.

Two trios showed transmission of the expanded AFF3 allele from a carrier parent to an affected proband; one maternal allele expanded from 133 to 822 copies and one paternal allele contracted from 424 to 157 copies, consistent with incomplete penetrance.

In 100kGP, long AFF3 alleles were enriched in 6,371 unsolved ID probands versus 8,794 ancestry-matched controls, with peak enrichment for alleles ≥61 copies (P=0.002; OR=3.9); 17/6,371 unsolved probands had ≥60-copy alleles versus 0/1,500 ID probands with other pathogenic findings.

Computational genotyping and association analyses linked the AFF3 GCC expansion to neurodevelopmental traits: ExpansionHunter identified long alleles, PheWAS associated expansions with reduced educational attainment, and local SNVs tagging the expansion overlapped GWAS signals for intelligence/cognitive ability.

Gene-level evidence: AFF3 is an AFF-family nuclear transcription-activating factor that forms super elongation complexes with active P-TEFb and AF9/ENL; the cited study did not directly test altered protein interactions caused by the FRA2A repeat.

The FRA2A CGG expansion lies in a brain-active alternative AFF3 promoter and is associated with local CpG hypermethylation and monoallelic AFF3 expression/silencing in carriers.

Patient-derived blood/lymphoblastoid material from FRA2A carriers showed expanded AFF3 CGG alleles with promoter hypermethylation; cSNP analysis in carrier BII.1 demonstrated monoallelic AFF3 expression.

Non-patient controls showed normal-range AFF3 CGG alleles and no methylation above threshold in control family samples, supporting that hypermethylation was specific to expansion carriers; this was comparator/control-cell evidence rather than an engineered expansion model.

Gene-level model evidence: whole-mount in situ hybridization showed mouse Aff3 expression in developing brain, somites, limb buds and palate; no non-human FRA2A repeat-expansion model was reported.