NM_000135.4(FANCA):c.3163C>T (p.Arg1055Trp) AND Fanconi anemia

Clinical significance:Pathogenic (Last evaluated: Nov 1, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000135.4(FANCA):c.3163C>T (p.Arg1055Trp)]

NM_000135.4(FANCA):c.3163C>T (p.Arg1055Trp)

FANCA:FA complementation group A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000135.4(FANCA):c.3163C>T (p.Arg1055Trp)
  • NC_000016.10:g.89749806G>A
  • NG_011706.1:g.71852C>T
  • NM_000135.4:c.3163C>TMANE SELECT
  • NM_001286167.3:c.3163C>T
  • NP_000126.2:p.Arg1055Trp
  • NP_001273096.1:p.Arg1055Trp
  • LRG_495t1:c.3163C>T
  • LRG_495:g.71852C>T
  • NC_000016.9:g.89816214G>A
  • NM_000135.2:c.3163C>T
Protein change:
dbSNP: rs753063086
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000135.4:c.3163C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001286167.3:c.3163C>T - missense variant - [Sequence Ontology: SO:0001583]


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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000949410Invitaecriteria provided, single submitter
(Nov 1, 2020)
germlineclinical testing

PubMed (9)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing



Four novel mutations of the Fanconi anemia group A gene (FAA) in Japanese patients.

Nakamura A, Matsuura S, Tauchi H, Hanada R, Ohashi H, Hasegawa T, Honda K, Masuno M, Imaizumi K, Sugita K, Ide T, Komatsu K.

J Hum Genet. 1999;44(1):48-51.

PubMed [citation]

Heterogeneous spectrum of mutations in the Fanconi anaemia group A gene.

Wijker M, Morgan NV, Herterich S, van Berkel CG, Tipping AJ, Gross HJ, Gille JJ, Pals G, Savino M, Altay C, Mohan S, Dokal I, Cavenagh J, Marsh J, van Weel M, Ortega JJ, Schuler D, Samochatova E, Karwacki M, Bekassy AN, Abecasis M, Ebell W, et al.

Eur J Hum Genet. 1999 Jan;7(1):52-9.

PubMed [citation]
See all PubMed Citations (9)

Details of each submission

From Invitae, SCV000949410.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (9)


This sequence change replaces arginine with tryptophan at codon 1055 of the FANCA protein (p.Arg1055Trp). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is present in population databases (rs753063086, ExAC 0.02%). This variant has been observed in individuals affected with Fanconi anemia (PMID: 9929978, 10094191, 15523645, 19367192). ClinVar contains an entry for this variant (Variation ID: 555008). This variant has been reported to affect FANCA protein function (PMID: 12444097, 24349332, 28864460). This variant disrupts the p.Arg1055 amino acid residue in FANCA. Other variant(s) that disrupt this residue have been observed in individuals with FANCA-related conditions (PMID: 24584348), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 6, 2021

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