FANCG

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

Basic information

Region (hg38): 9:35073834-35080004

Previous symbols: [ "XRCC9" ]

Links

ENSG00000221829 ∙ NCBI:2189 ∙ OMIM:602956 ∙ HGNC:3588 ∙ Uniprot:O15287 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Fanconi anemia, complementation group G	AR	Allergy/Immunology/Infectious; Cardiovascular; Hematologic; Oncologic	Specific 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 management	Audiologic/Otolaryngologic; Allergy/Immunology/Infectious; Cardiovascular; Dermatologic; Gastrointestinal; Hematologic; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic; Renal	9806548; 20301575

ClinVar

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

• Fanconi anemia (653 variants)
• Fanconi anemia complementation group G (240 variants)
• not provided (59 variants)
• not specified (43 variants)
• Inborn genetic diseases (12 variants)
• Ovarian cancer (8 variants)
• Amyotrophic Lateral Sclerosis, Dominant (6 variants)
• Inclusion Body Myopathy, Dominant (6 variants)
• FANCG-related condition (5 variants)
• Fanconi anemia complementation group A (2 variants)
• Pituitary stalk interruption syndrome (1 variants)
• Abnormality of blood and blood-forming tissues (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FANCG 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	206		211
missense		4	193	5	2	204
nonsense	28	17				45
start loss						0
frameshift	32	27	3			62
inframe indel		1	6			7
splice donor/acceptor (+/-2bp)	5	27				32
splice region		1	15	45	1	62
non coding			15	78	12	105
Total	65	76	222	289	14

Highest pathogenic variant AF is 0.0000791

Variants in FANCG

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

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

Position	Type	Phenotype	Significance	ClinVar
9-35073858-G-A		Fanconi anemia complementation group G	Uncertain significance (Jan 13, 2018)
9-35073967-T-C		Fanconi anemia complementation group G	Uncertain significance (Jan 12, 2018)
9-35074007-T-C		Fanconi anemia complementation group G	Uncertain significance (Jan 12, 2018)
9-35074031-G-A		Fanconi anemia complementation group G	Uncertain significance (Apr 27, 2017)
9-35074101-G-A		FANCG-related disorder	Likely benign (Apr 27, 2023)
9-35074112-A-G		not specified	Uncertain significance (Feb 14, 2020)
9-35074113-G-A		Fanconi anemia	Likely benign (Apr 28, 2022)
9-35074114-G-A		Fanconi anemia	Likely benign (Dec 30, 2023)
9-35074123-CTT-C		not specified • Fanconi anemia • Fanconi anemia complementation group G	Uncertain significance (Aug 10, 2022)
9-35074126-T-C		Fanconi anemia	Likely benign (Sep 15, 2021)
9-35074131-G-A		Fanconi anemia	Likely benign (May 15, 2023)
9-35074139-C-T			Uncertain significance (Jul 05, 2019)
9-35074140-G-A		Fanconi anemia	Uncertain significance (Aug 24, 2021)
9-35074151-AG-A		Fanconi anemia	Uncertain significance (Jul 30, 2022)
9-35074157-G-T		Fanconi anemia	Uncertain significance (Jan 25, 2024)
9-35074159-G-A		Fanconi anemia • Fanconi anemia complementation group G	Likely benign (Dec 01, 2023)
9-35074162-A-G		Fanconi anemia	Likely benign (Sep 27, 2023)
9-35074163-C-T		Fanconi anemia • Fanconi anemia complementation group G • Inborn genetic diseases	Uncertain significance (Jun 13, 2023)
9-35074164-G-A		Fanconi anemia complementation group G	Uncertain significance (Jul 18, 2022)
9-35074167-C-G		Fanconi anemia	Uncertain significance (Mar 24, 2022)
9-35074169-G-A		Fanconi anemia • Fanconi anemia complementation group G	Conflicting classifications of pathogenicity (Jan 18, 2024)
9-35074171-G-A		Fanconi anemia	Likely benign (Sep 17, 2023)
9-35074172-G-T		Fanconi anemia	Uncertain significance (Apr 18, 2019)
9-35074172-GGACGGATCCA-G		Fanconi anemia complementation group G • Fanconi anemia • FANCG-related disorder	Pathogenic (Feb 21, 2024)
9-35074173-G-A		Fanconi anemia	Uncertain significance (Sep 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FANCG	protein_coding	protein_coding	ENST00000378643	14	6182

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.49e-14	0.225	125638	0	110	125748	0.000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.245	301	313	0.961	0.0000182	3934
Missense in Polyphen		83	84.734	0.97954		1149
Synonymous	0.00585	138	138	0.999	0.00000740	1348
Loss of Function	1.15	25	32.0	0.781	0.00000151	366

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000667	0.000658
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.000194	0.000185
European (Non-Finnish)	0.000596	0.000580
Middle Eastern	0.000435	0.000435
South Asian	0.000393	0.000392
Other	0.000663	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA repair protein that may operate in a postreplication repair or a cell cycle checkpoint function. May be implicated in interstrand DNA cross-link repair and in the maintenance of normal chromosome stability. Candidate tumor suppressor gene.
• Pathway: Fanconi anemia pathway - Homo sapiens (human);Retinoblastoma (RB) in Cancer;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: 0.406

Intolerance Scores

• loftool: 0.873
• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.14

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.518
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.767

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fancg
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: ovarian follicle development;DNA repair;mitochondrion organization;spermatid development;response to radiation;interstrand cross-link repair
• Cellular component: nucleoplasm;nucleolus;mitochondrion;cytosol;plasma membrane;Fanconi anaemia nuclear complex
• Molecular function: damaged DNA binding;protein binding