FANCD2OS

FANCD2 opposite strand

Basic information

Region (hg38): 3:10081316-10108255

Previous symbols: [ "C3orf24" ]

Links

ENSG00000163705 ∙ NCBI:115795 ∙ ∙ HGNC:28623 ∙ Uniprot:Q96PS1 ∙ 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 FANCD2OS gene.

• Fanconi anemia (292 variants)
• Fanconi anemia complementation group D2 (104 variants)
• not provided (66 variants)
• not specified (25 variants)
• Inborn genetic diseases (18 variants)
• Hereditary breast ovarian cancer syndrome (15 variants)
• Fanconi anemia complementation group A (3 variants)
• Ovarian cancer (3 variants)
• Intellectual disability;Global developmental delay;Cleft palate (1 variants)
• Hereditary cancer (1 variants)
• Hepatoblastoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FANCD2OS 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						0
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	18	25	161	137	32	373
Total	18	25	166	137	32

Highest pathogenic variant AF is 0.0000197

Variants in FANCD2OS

This is a list of pathogenic ClinVar variants found in the FANCD2OS region.

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

Position	Type	Phenotype	Significance	ClinVar
3-10081327-A-T		Fanconi anemia	Likely benign (Oct 15, 2023)
3-10081331-C-A		Fanconi anemia	Likely benign (Oct 24, 2023)
3-10081331-C-G		Fanconi anemia	Likely benign (Aug 16, 2023)
3-10081331-C-T		Fanconi anemia	Likely benign (Aug 05, 2023)
3-10081332-A-C		Fanconi anemia	Likely benign (Nov 06, 2023)
3-10081332-A-G		Fanconi anemia	Likely benign (Jul 25, 2023)
3-10081333-T-C		Fanconi anemia	Likely benign (Feb 11, 2023)
3-10081333-T-G		Fanconi anemia • Fanconi anemia complementation group D2	Conflicting classifications of pathogenicity (Jan 04, 2024)
3-10081344-AGT-A		Fanconi anemia complementation group D2	Likely pathogenic (Aug 22, 2023)
3-10081346-T-A		Fanconi anemia	Uncertain significance (Aug 28, 2021)
3-10081348-T-C		Fanconi anemia	Likely benign (May 20, 2023)
3-10081366-C-T		Fanconi anemia • Fanconi anemia complementation group D2	Likely benign (Oct 16, 2023)
3-10081367-G-A		Fanconi anemia • Fanconi anemia complementation group D2	Uncertain significance (Jan 11, 2024)
3-10081379-G-A		Fanconi anemia	Uncertain significance (Oct 08, 2020)
3-10081389-T-A		Fanconi anemia • Fanconi anemia complementation group D2	Uncertain significance (Sep 17, 2022)
3-10081391-A-G		Fanconi anemia	Uncertain significance (Jul 17, 2023)
3-10081395-T-A		Fanconi anemia	Uncertain significance (Jun 05, 2023)
3-10081396-T-TGGAC		Fanconi anemia	Pathogenic (Jun 05, 2023)
3-10081403-T-C		not specified	Uncertain significance (Jan 21, 2016)
3-10081405-C-T		Fanconi anemia • Fanconi anemia complementation group D2 • FANCD2-related disorder	Likely benign (Jan 16, 2024)
3-10081409-A-G		Fanconi anemia	Uncertain significance (Feb 24, 2022)
3-10081412-A-G		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
3-10081421-T-C		Fanconi anemia	Uncertain significance (Oct 25, 2020)
3-10081425-ATCAGAGGC-A		Fanconi anemia	Pathogenic (Nov 14, 2021)
3-10081433-C-T		Fanconi anemia	Likely benign (Feb 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FANCD2OS	protein_coding	protein_coding	ENST00000450660	1	26915

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0227	0.780	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.323	90	99.0	0.909	0.00000532	1140
Missense in Polyphen		28	32.794	0.85381		392
Synonymous	0.897	33	40.2	0.820	0.00000214	361
Loss of Function	0.935	3	5.33	0.563	2.26e-7	62

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00158	0.00158
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.00158	0.00158
South Asian	0.000131	0.000131
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.364
• hipred: N
• hipred_score: 0.339
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fancd2os