DFFA

DNA fragmentation factor subunit alpha

Basic information

Region (hg38): 1:10456522-10472529

Links

ENSG00000160049 ∙ NCBI:1676 ∙ OMIM:601882 ∙ HGNC:2772 ∙ Uniprot:O00273 ∙ 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 DFFA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DFFA 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					1	1
missense			17	3	3	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	4

Variants in DFFA

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

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

Position	Type	Phenotype	Significance	ClinVar
1-10461512-C-T			Benign (Aug 15, 2018)
1-10461533-C-A		not specified	Uncertain significance (Jun 28, 2022)
1-10461560-A-G		not specified	Uncertain significance (Nov 29, 2021)
1-10461581-C-T		not specified	Uncertain significance (Sep 06, 2022)
1-10461586-C-T			Benign (Sep 29, 2017)
1-10461600-G-A			Likely benign (Sep 29, 2017)
1-10461606-C-T		not specified	Uncertain significance (May 30, 2024)
1-10461614-C-T		not specified	Likely benign (Feb 16, 2023)
1-10461641-G-A		not specified	Uncertain significance (Oct 06, 2023)
1-10463076-T-A			Benign (Mar 02, 2018)
1-10463090-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-10463093-C-G		not specified	Uncertain significance (Dec 28, 2022)
1-10463134-G-A		not specified	Uncertain significance (Nov 15, 2021)
1-10463143-G-A		not specified	Uncertain significance (Jun 13, 2023)
1-10463478-T-A		not specified	Uncertain significance (Sep 07, 2022)
1-10463533-G-C		not specified	Uncertain significance (Oct 26, 2021)
1-10463569-A-G			Benign (Mar 02, 2018)
1-10463586-T-G		not specified	Uncertain significance (Jun 27, 2022)
1-10467213-G-A		not specified	Uncertain significance (Aug 09, 2021)
1-10467242-T-C		not specified	Uncertain significance (Dec 21, 2022)
1-10467257-T-C		not specified	Uncertain significance (Aug 12, 2021)
1-10467261-A-C		not specified	Uncertain significance (Jan 07, 2022)
1-10467305-T-C		not specified	Uncertain significance (Apr 22, 2024)
1-10469185-T-C		not specified	Likely benign (Apr 25, 2022)
1-10469324-C-G		not specified	Uncertain significance (Mar 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DFFA	protein_coding	protein_coding	ENST00000377038	6	16005

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000866	0.793	125626	0	121	125747	0.000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.322	176	188	0.934	0.0000101	2134
Missense in Polyphen		45	57.2	0.78671		734
Synonymous	0.933	71	81.7	0.869	0.00000443	680
Loss of Function	1.17	8	12.4	0.643	5.27e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000452	0.000452
Ashkenazi Jewish	0.00606	0.00607
East Asian	0.00109	0.00109
Finnish	0.00	0.00
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.00109	0.00109
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitor of the caspase-activated DNase (DFF40).
• Pathway: Apoptosis - Homo sapiens (human);Apoptosis Modulation and Signaling;Apoptosis;Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation;Apoptotic Signaling Pathway;caspase cascade in apoptosis;granzyme a mediated apoptosis pathway;induction of apoptosis through dr3 and dr4/5 death receptors;hiv-1 nef: negative effector of fas and tnf;apoptotic dna-fragmentation and tissue homeostasis;Activation of DNA fragmentation factor;Apoptosis induced DNA fragmentation;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Caspase Cascade in Apoptosis;HIV-1 Nef: Negative effector of Fas and TNF-alpha (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.148
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.1

Haploinsufficiency Scores

• pHI: 0.257
• hipred: N
• hipred_score: 0.457
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0000508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dffa
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: apoptotic DNA fragmentation;negative regulation of deoxyribonuclease activity;positive regulation of apoptotic process;chaperone-mediated protein folding;thymocyte apoptotic process;negative regulation of execution phase of apoptosis;negative regulation of apoptotic DNA fragmentation
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;lipid droplet;cytosol;plasma membrane
• Molecular function: protein binding;protein domain specific binding;protein folding chaperone;deoxyribonuclease inhibitor activity