AFDN

afadin, adherens junction formation factor, the group of PDZ domain containing

Basic information

Region (hg38): 6:167826893-167972023

Previous symbols: [ "MLLT4" ]

Links

ENSG00000130396 ∙ NCBI:4301 ∙ OMIM:159559 ∙ HGNC:7137 ∙ Uniprot:P55196 ∙ 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 AFDN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AFDN 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				3	1	4
missense			12			12
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	3	1

Variants in AFDN

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

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

Position	Type	Phenotype	Significance	ClinVar
6-167875472-G-A		not specified	Uncertain significance (Oct 05, 2021)
6-167880511-C-T			Likely benign (Sep 01, 2022)
6-167896967-A-G		not specified	Uncertain significance (Mar 25, 2015)
6-167902355-T-C		not specified	Uncertain significance (Aug 02, 2021)
6-167911425-A-G		not specified	Uncertain significance (Aug 12, 2021)
6-167915425-ATC-TGA		not specified	Uncertain significance (Jan 12, 2017)
6-167922943-G-A		not specified	Uncertain significance (Mar 20, 2024)
6-167946829-C-G		not specified	Uncertain significance (Oct 26, 2021)
6-167946832-A-G		not specified	Uncertain significance (Jan 30, 2024)
6-167946876-T-A		not specified	Uncertain significance (Jul 06, 2021)
6-167948301-G-A			Benign (Oct 24, 2017)
6-167951286-T-C		not specified	Uncertain significance (Oct 26, 2021)
6-167951581-G-A			Likely benign (Aug 01, 2022)
6-167951759-A-G		not specified	Uncertain significance (Aug 10, 2021)
6-167951901-A-C		not specified	Uncertain significance (Nov 15, 2021)
6-167962500-G-T		not specified	Uncertain significance (Nov 09, 2021)
6-167965849-G-C			Likely benign (Oct 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AFDN	protein_coding	protein_coding	ENST00000392108	30	145102

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000175	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	771	964	0.800	0.0000576	10844
Missense in Polyphen		299	452.81	0.66032		5140
Synonymous	-0.571	367	353	1.04	0.0000211	3148
Loss of Function	7.47	11	85.5	0.129	0.00000490	967

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.0000854	0.0000791
Middle Eastern	0.000163	0.000163
South Asian	0.0000653	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Belongs to an adhesion system, probably together with the E-cadherin-catenin system, which plays a role in the organization of homotypic, interneuronal and heterotypic cell-cell adherens junctions (AJs). Nectin- and actin-filament-binding protein that connects nectin to the actin cytoskeleton.
• Disease: DISEASE: Note=A chromosomal aberration involving AFDN is associated with acute leukemias. Translocation t(6;11)(q27;q23) with KMT2A/MLL1. The result is a rogue activator protein.
• Pathway: Adherens junction - Homo sapiens (human);Tight junction - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);VEGFA-VEGFR2 Signaling Pathway;Ras Signaling;SHP2 signaling;Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication;Stabilization and expansion of the E-cadherin adherens junction;Nectin adhesion pathway;PDGFR-beta signaling pathway;E-cadherin signaling in the nascent adherens junction (Consensus)

Recessive Scores

• pRec: 0.378

Intolerance Scores

• rvis_EVS: -2.36
• rvis_percentile_EVS: 1.14

Haploinsufficiency Scores

• pHI: 0.846
• hipred: Y
• hipred_score: 0.793
• ghis: 0.576

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Afdn
• 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); embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region 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); cellular phenotype

Gene ontology

• Biological process: cell adhesion;signal transduction;cell-cell signaling;negative regulation of cell migration;regulation of protein localization;adherens junction organization;positive regulation of GTPase activity;cell-cell adhesion mediated by cadherin;establishment of protein localization to plasma membrane;bicellular tight junction assembly;establishment of endothelial intestinal barrier;positive regulation of cell-cell adhesion mediated by cadherin
• Cellular component: nucleoplasm;cytosol;plasma membrane;cell-cell junction;cell-cell adherens junction;nuclear speck;cell junction;cell-cell contact zone;tight junction
• Molecular function: protein binding;protein C-terminus binding;Ras GTPase binding;cadherin binding;cell adhesion molecule binding;actin filament binding