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FANCA

FA complementation group A, the group of FA core complex|FA complementation groups

Basic information

Region (hg38): 16:89726683-89816977

Previous symbols: [ "FACA", "FANCH" ]

Links

ENSG00000187741 ∙ NCBI:2175 ∙ OMIM:607139 ∙ HGNC:3582 ∙ Uniprot:O15360 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 40.

Transcript IDProtein IDCoding exonsMANE SelectMANE Plus Clinical
NM_000135.4NP_000126.243yes-
ENST00000389301.8ENSP00000373952.343yes-
NM_001018112.3NP_001018122.111--
NM_001286167.3NP_001273096.143--

Phenotypes

GenCC

Source: genCC

  • Fanconi anemia complementation group A (Definitive), mode of inheritance: AR
  • Fanconi anemia complementation group A (Definitive), mode of inheritance: AR
  • Fanconi anemia complementation group A (Strong), mode of inheritance: AR
  • Fanconi anemia complementation group A (Strong), mode of inheritance: AR
  • Fanconi anemia complementation group A (Definitive), mode of inheritance: AR
  • Fanconi anemia (Supportive), mode of inheritance: AR
  • Fanconi anemia complementation group A (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Fanconi anemia, complementation group AARAllergy/Immunology/Infectious; Cardiovascular; Hematologic; OncologicSpecific treatments can help manifestations (eg, oral androgens for blood counts; G-CSF for neutrophil count); HSCT can be curative, but solid tumor risk may remain; Surveillance for complications such as bone marrow failure is recommended; Fanconi anemia can involve congenital cardiac (and other) anomalies, and awareness may allow early managementAudiologic/Otolaryngologic; Allergy/Immunology/Infectious; Cardiovascular; Dermatologic; Gastrointestinal; Hematologic; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic; Renal13826667; 6338978; 2571931; 1536187; 1521091; 8502512; 8081006; 8781414; 9371798; 10094191; 11389461; 14504102; 14605744; 17105750; 20301575; 20507306; 21273304; 22480464; 22950077; 23067021; 23898106; 23973728
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ClinVar

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

  • Fanconi_anemia (4440 variants)
  • Inborn_genetic_diseases (2397 variants)
  • Fanconi_anemia_complementation_group_A (1565 variants)
  • not_provided (867 variants)
  • not_specified (250 variants)
  • FANCA-related_disorder (201 variants)
  • Ovarian_cancer (10 variants)
  • Hereditary_cancer-predisposing_syndrome (5 variants)
  • See_cases (4 variants)
  • Neuroblastoma (2 variants)
  • Microcephaly (2 variants)
  • Diffuse_pediatric-type_high-grade_glioma,_H3-wildtype_and_IDH-wildtype (2 variants)
  • Abnormality_of_blood_and_blood-forming_tissues (2 variants)
  • Pituitary_stalk_interruption_syndrome (1 variants)
  • Congenital_portosystemic_shunt (1 variants)
  • Premature_ovarian_failure (1 variants)
  • Monogenic_short_statue (1 variants)
  • Pediatric_high-grade_glioma (1 variants)
  • Neurodevelopmental_abnormality (1 variants)
  • Hepatoblastoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FANCA gene is commonly pathogenic or not. These statistics are base on transcript: NM_000135.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
2
clinvar
43
clinvar
1318
clinvar
6
clinvar
 1374
missense
33
clinvar
78
clinvar
2410
clinvar
220
clinvar
4
clinvar
 2745
nonsense
128
clinvar
107
clinvar
5
clinvar
 240
start loss
3
7
10
frameshift
210
clinvar
158
clinvar
10
clinvar
 378
splice donor/acceptor (+/-2bp)
84
clinvar
166
clinvar
18
clinvar
1
clinvar
 269
Total 463 518 2486 1539 10

Highest pathogenic variant AF is 0.00012729385

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
FANCAprotein_codingprotein_codingENST00000389301 4379109
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
12547802701257480.00107
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-5.4112027771.550.00004829398
Missense in Polyphen4131.2811.3107289
Synonymous-8.035063221.570.00002182907
Loss of Function-1.299683.31.150.00000424952

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002400.00240
Ashkenazi Jewish0.00009930.0000992
East Asian0.001480.00147
Finnish0.0001850.000185
European (Non-Finnish)0.001260.00126
Middle Eastern0.001480.00147
South Asian0.001140.00114
Other0.0004890.000489

dbNSFP

Source: dbNSFP

Function
FUNCTION: DNA repair protein that may operate in a postreplication repair or a cell cycle checkpoint function. May be involved in interstrand DNA cross-link repair and in the maintenance of normal chromosome stability.;
Disease
DISEASE: Fanconi anemia, complementation group A (FANCA) [MIM:227650]: A disorder affecting all bone marrow elements and resulting in anemia, leukopenia and thrombopenia. It is associated with cardiac, renal and limb malformations, dermal pigmentary changes, and a predisposition to the development of malignancies. At the cellular level it is associated with hypersensitivity to DNA-damaging agents, chromosomal instability (increased chromosome breakage) and defective DNA repair. {ECO:0000269|PubMed:10094191, ECO:0000269|PubMed:10210316, ECO:0000269|PubMed:10521298, ECO:0000269|PubMed:10807541, ECO:0000269|PubMed:11091222, ECO:0000269|PubMed:17924555, ECO:0000269|PubMed:9371798, ECO:0000269|PubMed:9399890, ECO:0000269|PubMed:9929978}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Fanconi anemia pathway - Homo sapiens (human);Fanconi Anemia Pathway;DNA Repair;role of brca1 brca2 and atr in cancer susceptibility;brca1 dependent ub ligase activity;Fanconi anemia pathway;BARD1 signaling events (Consensus)

Recessive Scores

pRec
0.243

Intolerance Scores

loftool
0.0821
rvis_EVS
-0.1
rvis_percentile_EVS
45.67

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.985

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
DNA repair;male meiotic nuclear division;male gonad development;female gonad development;interstrand cross-link repair;regulation of cell population proliferation;regulation of regulatory T cell differentiation;regulation of inflammatory response;regulation of DNA-binding transcription factor activity;protein-containing complex assembly;regulation of CD40 signaling pathway
Cellular component
nucleus;nucleoplasm;cytoplasm;Fanconi anaemia nuclear complex
Molecular function
protein binding
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