NM_000135.4(FANCA):c.4015C>T (p.Leu1339Phe) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jan 12, 2023
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:: RCV003477510.1

Allele description [Variation Report for NM_000135.4(FANCA):c.4015C>T (p.Leu1339Phe)]

NM_000135.4(FANCA):c.4015C>T (p.Leu1339Phe)

Genes:

FANCA:FA complementation group A [Gene - OMIM - HGNC]
ZNF276:zinc finger protein 276 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q24.3

Genomic location:

Preferred name:

NM_000135.4(FANCA):c.4015C>T (p.Leu1339Phe)

Other names:

p.Leu1339Phe

HGVS:

NC_000016.10:g.89739285G>A
NG_011706.1:g.82373C>T
NM_000135.4:c.4015C>TMANE SELECT
NM_001113525.2:c.*1039G>AMANE SELECT
NM_001286167.3:c.4015C>T
NM_152287.4:c.*1039G>A
NP_000126.2:p.Leu1339Phe
NP_000126.2:p.Leu1339Phe
NP_001273096.1:p.Leu1339Phe
LRG_495t1:c.4015C>T
LRG_495:g.82373C>T
LRG_495p1:p.Leu1339Phe
NC_000016.9:g.89805693G>A
NM_000135.2:c.4015C>T
NM_000135.3:c.4015C>T
NR_110122.2:n.3039G>A
NR_110126.2:n.2922G>A
NR_110128.2:n.2862G>A
NR_110129.2:n.2956G>A

Protein change:

L1339F

Links:

dbSNP: rs149775657

NCBI 1000 Genomes Browser:

rs149775657

Molecular consequence:

NM_001113525.2:c.*1039G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_152287.4:c.*1039G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000135.4:c.4015C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001286167.3:c.4015C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_110122.2:n.3039G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_110126.2:n.2922G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_110128.2:n.2862G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_110129.2:n.2956G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004218598	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Jan 12, 2023)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 24728327, 31698007, 26467025
SCV004224278	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 13, 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

SCV004218598

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Uncertain significance
(Jan 12, 2023)

unknown

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV004224278

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 13, 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	1	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

Nothing to display

See all PubMed Citations (4)

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004218598.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

The frequency of this variant in the general population, 0.00028 (7/24954 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported only in a healthy individual (PMID: 24728327 (2014)) and as a somatic variant in an individual with prostate cancer (PMID: 31698007 (2019)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is benign or damaging. Based on the available information, we are unable to determine the clinical significance of this variant.

#	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

From Mayo Clinic Laboratories, Mayo Clinic, SCV004224278.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	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	germline	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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