NM_021922.3(FANCE):c.1309A>G (p.Met437Val) AND Fanconi anemia complementation group E

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 20, 2022
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:: RCV000543258.4

Allele description [Variation Report for NM_021922.3(FANCE):c.1309A>G (p.Met437Val)]

NM_021922.3(FANCE):c.1309A>G (p.Met437Val)

Gene:

FANCE:FA complementation group E [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p21.31

Genomic location:

Preferred name:

NM_021922.3(FANCE):c.1309A>G (p.Met437Val)

HGVS:

NC_000006.12:g.35459753A>G
NG_011708.1:g.12393A>G
NM_021922.3:c.1309A>GMANE SELECT
NP_068741.1:p.Met437Val
NP_068741.1:p.Met437Val
LRG_498t1:c.1309A>G
LRG_498:g.12393A>G
LRG_498p1:p.Met437Val
NC_000006.11:g.35427530A>G
NM_021922.2:c.1309A>G

Protein change:

M437V

Links:

dbSNP: rs746770705

NCBI 1000 Genomes Browser:

rs746770705

Molecular consequence:

NM_021922.3:c.1309A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Fanconi anemia complementation group E (FANCE)
Identifiers:: MONDO: MONDO:0010953; MedGen: C3160739; Orphanet: 84; OMIM: 600901

Recent activity

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Fungal sp. E14726J 18S ribosomal RNA gene, partial sequence; internal transcribe...
Fungal sp. E14726J 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
gi|705806030|gb|KM265667.1|

Nucleotide
sugar ABC transporter substrate-binding protein [Thermus brockianus]
sugar ABC transporter substrate-binding protein [Thermus brockianus]
gi|1102956653|gnl|XXX|A0O31_01570|g 09679.1|

Protein
PREDICTED: glycogen synthase kinase-3 beta-like isoform X2 [Dufourea novaeanglia...
PREDICTED: glycogen synthase kinase-3 beta-like isoform X2 [Dufourea novaeangliae]
gi|987920518|ref|XP_015436375.1|

Protein
"Gilbert Disease" (2755)
Books
conserved hypothetical protein [Streptosporangium roseum DSM 43021]
conserved hypothetical protein [Streptosporangium roseum DSM 43021]
gi|270511097|gnl|jgi|Sros_6665|gb|A 75.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000650809	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 20, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002814129	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 4, 2022)	unknown	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

SCV000650809

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 20, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002814129

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 4, 2022)

unknown

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	unknown	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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

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 Invitae, SCV000650809.3

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

Description

This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 437 of the FANCE protein (p.Met437Val). This variant is present in population databases (rs746770705, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with FANCE-related conditions. ClinVar contains an entry for this variant (Variation ID: 471919). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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.

#	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 Fulgent Genetics, Fulgent Genetics, SCV002814129.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 7, 2023

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