Locus FRA2A AFF3
Disease ID
FRA2A
Gene ID
AFF3
Updated
Jun 24, 2026
v2.23.0
v2.23.0
Other gene loci
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Bioinformatical Links
Disease
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Name Intellectual disability associated with fragile site FRA2A
Inheritance
Description These expansions are associated with intellectual disability and clinical phenotypes such as delayed motor development or delays in speech/language1 .
Prevalence
Age of Onset Early childhood (small sample size)1 .
HPO Terms
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Association
MendelianRisk
Locus
Details Allele ranges established in study of 3 families; intermediate alleles likely premutations1 . Pathogenic threshold may be higher than 300 as this was the largest allele that could be accurately sized by the assay.
Mechanism Silencing of the FMR2 gene as a consequence of a CCG expansion located upstream of this gene3 .
LoF/methylation
Detection
Year Year first published 20141
Location in Gene
Intron 3
Gene Strand
Alleles
Ref. Motif Reference motif, reference orientation
CCG
Ranges
Benign (ref.) Benign motif, reference orientation
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Benign (gene) Benign motif, gene orientation
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Pathogenic (ref.) Pathogenic motif, reference orientation
CCG
Pathogen. (gene) Pathogenic motif, gene orientation
CGG
Unknown (ref.) Unknown motif, reference orientation
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Unknown (gene) Unknown motif, gene orientation
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Interruption (ref.) Interruption motif, reference orientation
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Interrup. (gene) Interruption motif, gene orientation
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References
Direct supporting references for info on this page.
1
FRA2A is a CGG repeat expansion associated with silencing of AFF3.
Sofie,Metsu, Liesbeth,Rooms, Jacqueline,Rainger, Martin S,Taylor, Hemant,Bengani, David I,Wilson, Chandra Sekhar Reddy,Chilamakuri, Harris,Morrison, Geert,Vandeweyer, Edwin,Reyniers, Evelyn,Douglas, Geoffrey,Thompson, Eric,Haan, Jozef,Gecz, David R,Fitzpatrick, R Frank,Kooy
PLoS genetics · 2014-04-24
pmid:247632822
A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 associated with intellectual disability.
Bharati,Jadhav, Paras,Garg, Joke J F A,van Vugt, Kristina,Ibanez, Delia,Gagliardi, William,Lee, Mariya,Shadrina, Tom,Mokveld, Egor,Dolzhenko, Alejandro,Martin-Trujillo, Scott J,Gies, Gabrielle,Altman, Clarissa,Rocca, Mafalda,Barbosa, Miten,Jain, Nayana,Lahiri, Katherine,Lachlan, Henry,Houlden, Benedict,Paten, Jan,Veldink, Arianna,Tucci, Andrew J,Sharp
Nature genetics · 2024-09-23
pmid:39313615Additional Literature
Additional literature related to this locus.
Raw PubMed search results
(All PubMed results returned by searching for this gene, tandem
repeats, and disease, in medline format)
A genome-wide approach for the discovery of novel repeat expansion disorders in the Undiagnosed Diseases Network cohort.
Sarah,Fazal, Harriet,Dashnow, Maike F,Dohrn, Jacquelyn,Raposo, Laurel,Hiatt, Matt C,Danzi, Isaac R L,Xu, Camilo,Toro, David R,Adams, Karen,Usdin, Bruce,Hayward, Shilpa Nadimpalli,Kobren, Shamil R,Sunyaev, Rebecca C,Spillmann, Vandana,Shashi, Adriana,Rebelo, Guney,Bademci, Mustafa,Tekin, Aaron R,Quinlan, Stephan,Zuchner
Genetics in medicine : official journal of the American College of Medical Genetics · 2025-05-22
pmid:40417743A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in
Bharati,Jadhav, Paras,Garg, Joke J F A,van Vugt, Kristina,Ibanez, Delia,Gagliardi, William,Lee, Mariya,Shadrina, Tom,Mokveld, Egor,Dolzhenko, Alejandro,Martin-Trujillo, Scott L,Gies, Clarissa,Rocca, Mafalda,Barbosa, Miten,Jain, Nayana,Lahiri, Katherine,Lachlan, Henry,Houlden, Benedict,Paten, Jan,Veldink, Arianna,Tucci, Andrew J,Sharp
medRxiv : the preprint server for health sciences · 2023-12-12
pmid:37205357