NM_000135.4(FANCA):c.390G>T (p.Glu130Asp) AND Fanconi anemia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 10, 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:: RCV002690607.2

Allele description [Variation Report for NM_000135.4(FANCA):c.390G>T (p.Glu130Asp)]

NM_000135.4(FANCA):c.390G>T (p.Glu130Asp)

Gene:

FANCA:FA complementation group A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q24.3

Genomic location:

Preferred name:

NM_000135.4(FANCA):c.390G>T (p.Glu130Asp)

HGVS:

NC_000016.10:g.89810965C>A
NG_011706.1:g.10693G>T
NM_000135.4:c.390G>TMANE SELECT
NM_001018112.3:c.390G>T
NM_001286167.3:c.390G>T
NM_001351830.2:c.390G>T
NP_000126.2:p.Glu130Asp
NP_000126.2:p.Glu130Asp
NP_001018122.1:p.Glu130Asp
NP_001273096.1:p.Glu130Asp
NP_001338759.1:p.Glu130Asp
LRG_495t1:c.390G>T
LRG_495:g.10693G>T
LRG_495p1:p.Glu130Asp
NC_000016.9:g.89877373C>A
NM_000135.2:c.390G>T

Protein change:

E130D

Molecular consequence:

NM_000135.4:c.390G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001018112.3:c.390G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001286167.3:c.390G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001351830.2:c.390G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

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nuclear distribution protein [Nannochloropsis gaditana CCMP526]
nuclear distribution protein [Nannochloropsis gaditana CCMP526]
gi|553187340|ref|XP_005854589.1|

Protein
hypothetical protein AURANDRAFT_27356 [Aureococcus anophagefferens]
hypothetical protein AURANDRAFT_27356 [Aureococcus anophagefferens]
gi|676388975|ref|XP_009037766.1||gn _WGS:ACJI|AURANDRAFT_27356

Protein
LOC108663711 [Theobroma cacao]
LOC108663711 [Theobroma cacao]
Gene ID:108663711

Gene
108663711[uid] AND (alive[prop]) (1)
Gene
Baccharis schomburgkii (0)
Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002991347	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 10, 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

SCV002991347

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 10, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002991347.1

#	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 glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 130 of the FANCA protein (p.Glu130Asp). This variant is present in population databases (rs781401861, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with FANCA-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt FANCA protein function. 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

Last Updated: Sep 29, 2024

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