NM_001018115.3(FANCD2):c.2605+1G>A AND Fanconi anemia complementation group D2

Germline classification:: Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:: Mar 25, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001332747.8

Allele description [Variation Report for NM_001018115.3(FANCD2):c.2605+1G>A]

NM_001018115.3(FANCD2):c.2605+1G>A

Genes:

VHL:von Hippel-Lindau tumor suppressor [Gene - OMIM - HGNC]
LOC107303338:3p25 FANCD2 Alu-mediated recombination region [Gene]
FANCD2:FA complementation group D2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.3

Genomic location:

Preferred name:

NM_001018115.3(FANCD2):c.2605+1G>A

HGVS:

NC_000003.12:g.10072982G>A
NG_007311.1:g.51554G>A
NG_046754.1:g.42136G>A
NM_001018115.3:c.2605+1G>AMANE SELECT
NM_001319984.2:c.2605+1G>A
NM_001374253.1:c.2494+1G>A
NM_001374254.1:c.2605+1G>A
NM_033084.6:c.2605+1G>A
LRG_306t2:c.2605+1G>A
LRG_306:g.51554G>A
NC_000003.11:g.10114666G>A
NM_033084.3:c.2605+1G>A
NM_033084.5:c.2605+1G>A

Links:

dbSNP: rs142365855

NCBI 1000 Genomes Browser:

rs142365855

Molecular consequence:

NM_001018115.3:c.2605+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001319984.2:c.2605+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374253.1:c.2494+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374254.1:c.2605+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_033084.6:c.2605+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Fanconi anemia complementation group D2
Synonyms:: FANCONI PANCYTOPENIA, TYPE 4; FANCONI ANEMIA, COMPLEMENTATION GROUP D
Identifiers:: MONDO: MONDO:0009214; MedGen: C3160738; Orphanet: 84; OMIM: 227646

Recent activity

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Mus musculus paraoxonase 1 (Pon1), transcript variant 2, mRNA
Mus musculus paraoxonase 1 (Pon1), transcript variant 2, mRNA
gi|2280970852|ref|NM_001410259.1|

Nucleotide
PREDICTED: Mus musculus SH3-binding kinase 1 (Sbk1), transcript variant X1, mRNA
PREDICTED: Mus musculus SH3-binding kinase 1 (Sbk1), transcript variant X1, mRNA
gi|1907176441|ref|XM_036152556.1|

Nucleotide
mitogen-activated protein kinase kinase kinase 13 isoform X1 [Mus musculus]
mitogen-activated protein kinase kinase kinase 13 isoform X1 [Mus musculus]
gi|755554055|ref|XP_011244317.1|

Protein
F-box/WD repeat-containing protein 5 isoform 3 [Mus musculus]
F-box/WD repeat-containing protein 5 isoform 3 [Mus musculus]
gi|1249618468|ref|NP_001343337.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001525154	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jul 31, 2019)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002022344	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 11, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004102668	Daryl Scott Lab, Baylor College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 10, 2023)	maternal	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004806334	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 25, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	maternal	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Baylor Genetics, SCV001525154.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant was determined to be likely pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV002022344.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Daryl Scott Lab, Baylor College of Medicine, SCV004102668.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004806334.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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