AFF1

ALF transcription elongation factor 1, the group of Super elongation complex|AF4/FMR2 family

Basic information

Region (hg38): 4:86935002-87141039

Previous symbols: [ "PBM1", "MLLT2" ]

Links

ENSG00000172493 ∙ NCBI:4299 ∙ OMIM:159557 ∙ HGNC:7135 ∙ Uniprot:P51825 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AFF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AFF1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	2	7
missense			81	7	1	89
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	81	12	3

Variants in AFF1

This is a list of pathogenic ClinVar variants found in the AFF1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-87046171-A-G		not specified	Uncertain significance (Mar 21, 2023)
4-87046174-A-G		not specified	Uncertain significance (Jan 26, 2022)
4-87046207-A-G		not specified	Uncertain significance (Aug 02, 2022)
4-87046239-A-G		not specified	Uncertain significance (Mar 28, 2024)
4-87046247-A-G			Benign (Jul 23, 2018)
4-87046696-C-T		not specified	Uncertain significance (Dec 01, 2022)
4-87046720-G-A		not specified	Uncertain significance (Oct 14, 2023)
4-87046750-A-G		not specified	Uncertain significance (May 08, 2023)
4-87046759-A-G		not specified	Uncertain significance (Apr 04, 2024)
4-87046774-C-T		not specified	Uncertain significance (Aug 17, 2022)
4-87046791-C-T		not specified	Uncertain significance (Dec 21, 2022)
4-87046792-G-A		not specified	Uncertain significance (Mar 01, 2024)
4-87046825-C-T		not specified	Uncertain significance (Apr 07, 2023)
4-87046891-A-G		not specified	Uncertain significance (May 08, 2024)
4-87046915-C-T		not specified	Uncertain significance (Mar 28, 2023)
4-87047068-C-G		not specified	Uncertain significance (Aug 08, 2023)
4-87047102-C-T			Likely benign (Apr 04, 2018)
4-87047119-C-T		not specified	Likely benign (May 20, 2024)
4-87047152-C-T		not specified	Uncertain significance (Jan 09, 2024)
4-87047250-G-A		not specified	Likely benign (Sep 14, 2023)
4-87047257-G-A		not specified	Likely benign (Mar 17, 2023)
4-87047275-A-G		not specified	Likely benign (Jan 26, 2022)
4-87047340-A-G		not specified	Uncertain significance (Sep 22, 2022)
4-87047410-C-T		not specified	Uncertain significance (Jun 30, 2022)
4-87047416-A-T		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AFF1	protein_coding	protein_coding	ENST00000395146	20	206053

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.710	0.290	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.406	700	670	1.04	0.0000381	7979
Missense in Polyphen		131	116.93	1.1203		1508
Synonymous	-2.40	311	262	1.19	0.0000159	2399
Loss of Function	5.30	11	52.5	0.210	0.00000271	658

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000216	0.000215
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.000163	0.000163
South Asian	0.000229	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=A chromosomal aberration involving AFF1 is associated with acute leukemias. Translocation t(4;11)(q21;q23) with KMT2A/MLL1. The result is a rogue activator protein.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.185

Intolerance Scores

• loftool: 0.657
• rvis_EVS: -1.18
• rvis_percentile_EVS: 5.91

Haploinsufficiency Scores

• pHI: 0.0974
• hipred: N
• hipred_score: 0.493
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.928

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Aff1
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; hematopoietic system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: regulation of transcription, DNA-templated
• Cellular component: nucleus;transcription elongation factor complex;ELL-EAF complex
• Molecular function: double-stranded DNA binding;DNA-binding transcription factor activity;protein binding