NM_018062.4(FANCL):c.1033CTA[1] (p.Leu346del) AND Fanconi anemia

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 21, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV002907801.2

Allele description

NM_018062.4(FANCL):c.1033CTA[1] (p.Leu346del)

Gene:

FANCL:FA complementation group L [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

2p16.1

Genomic location:

Preferred name:

NM_018062.4(FANCL):c.1033CTA[1] (p.Leu346del)

HGVS:

NC_000002.12:g.58160163AGT[1]
NG_007418.1:g.86213CTA[1]
NG_029717.2:g.257423AGT[1]
NM_001114636.2:c.1047_1049ACT[1]
NM_001374615.1:c.1078CTA[1]
NM_001410792.1:c.1093CTA[1]
NM_018062.4:c.1033CTA[1]MANE SELECT
NP_001108108.1:p.Leu351del
NP_001108108.1:p.Leu351del
NP_001361544.1:p.Leu361del
NP_001397721.1:p.Leu366del
NP_060532.2:p.Leu346del
NP_060532.2:p.Leu346del
LRG_501t1:c.1048CTA[1]
LRG_501t2:c.1032_1034ACT[1]
LRG_501:g.86213CTA[1]
LRG_501p1:p.Leu351del
LRG_501p2:p.Leu346del
NC_000002.11:g.58387297_58387299del
NC_000002.11:g.58387298AGT[1]
NM_001114636.1:c.1048CTA[1]
NM_018062.3:c.1032_1034ACT[1]
NR_156742.1:n.822CTA[1]
NR_156742.2:n.766_768ACT[1]
NR_164659.1:n.914CTA[1]
NR_164659.2:n.931_933ACT[1]

Protein change:

L346del

Molecular consequence:

NM_001374615.1:c.1078CTA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001410792.1:c.1093CTA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_018062.4:c.1033CTA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001114636.2:c.1047_1049ACT[1] - inframe_indel - [Sequence Ontology: SO:0001820]

Condition(s)

Name:: Fanconi anemia (FA)
Synonyms:: Fanconi pancytopenia; Fanconi's anemia
Identifiers:: MONDO: MONDO:0019391; MeSH: D005199; MedGen: C0015625; Orphanet: 84; OMIM: PS227650

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003244842	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 21, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003244842

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 21, 2022)

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003244842.2

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with FANCL-related conditions. This variant is present in population databases (rs763041336, gnomAD 0.003%). This variant, c.1036_1038del, results in the deletion of 1 amino acid(s) of the FANCL protein (p.Leu346del), but otherwise preserves the integrity of the reading frame.

#	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: Feb 20, 2024

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