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NM_000135.4(FANCA):c.4015del (p.Leu1339fs)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 13, 2020
Accession:
VCV000208638.5
Variation ID:
208638
Description:
1bp deletion
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NM_000135.4(FANCA):c.4015del (p.Leu1339fs)

Allele ID
205212
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
16q24.3
Genomic location
16: 89739285 (GRCh38) GRCh38 UCSC
16: 89805693 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_495:g.82373del
LRG_495t1:c.4015del
NC_000016.10:g.89739285del
... more HGVS
Protein change
L1339fs
Other names
-
Canonical SPDI
NC_000016.10:89739284:G:
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00001
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Links
ClinGen: CA276031
dbSNP: rs762902309
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Nov 2, 2016 RCV000190642.2
Pathogenic 1 criteria provided, single submitter Oct 13, 2020 RCV001043860.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
FANCA - - GRCh38
GRCh37
2154 2635
ZNF276 - - GRCh38
GRCh37
- 420

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jan 01, 2014)
criteria provided, single submitter
Method: research
Fanconi anemia, complementation group A
Allele origin: germline
Center for Individualized Medicine,Mayo Clinic
Study: Breast Cancer Genome Guided Therapy Study (BEAUTY)
Accession: SCV000245685.2
Submitted: (Sep 10, 2015)
Evidence details
Publications
PubMed (1)
Likely pathogenic
(Nov 02, 2016)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia, complementation group A
Allele origin: unknown
Counsyl
Accession: SCV000486569.1
Submitted: (Nov 23, 2016)
Evidence details
Publications
PubMed (1)
Pathogenic
(Oct 13, 2020)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia
Allele origin: germline
Invitae
Accession: SCV001207627.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change creates a premature translational stop signal (p.Leu1339Serfs*24) in the FANCA gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Feb 28, 2020)
no assertion criteria provided
Method: curation
Fanconi anemia, complementation group A
Allele origin: germline
Leiden Open Variation Database
Accession: SCV001425727.1
Submitted: (Mar 04, 2020)
Evidence details
Publications
PubMed (1)
Comment:
Curator: Arleen D. Auerbach. Submitter to LOVD: Arleen D. Auerbach.

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
A comprehensive approach to identification of pathogenic FANCA variants in Fanconi anemia patients and their families. Kimble DC Human mutation 2018 PMID: 29098742
Exome sequencing reveals frequent deleterious germline variants in cancer susceptibility genes in women with invasive breast cancer undergoing neoadjuvant chemotherapy. Ellingson MS Breast cancer research and treatment 2015 PMID: 26296701
Validation of Fanconi anemia complementation Group A assignment using molecular analysis. Moghrabi NN Genetics in medicine : official journal of the American College of Medical Genetics 2009 PMID: 19367192
High frequency of large intragenic deletions in the Fanconi anemia group A gene. Morgan NV American journal of human genetics 1999 PMID: 10521298

Text-mined citations for rs762902309...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 24, 2021