NM_000136.3(FANCC):c.1394A>G (p.Gln465Arg) AND not provided

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Apr 29, 2016
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:: RCV000590373.13

Allele description [Variation Report for NM_000136.3(FANCC):c.1394A>G (p.Gln465Arg)]

NM_000136.3(FANCC):c.1394A>G (p.Gln465Arg)

Genes:

FANCC:FA complementation group C [Gene - OMIM - HGNC]
AOPEP:aminopeptidase O (putative) [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q22.32

Genomic location:

Preferred name:

NM_000136.3(FANCC):c.1394A>G (p.Gln465Arg)

Other names:

p.Q465R:CAG>CGG

HGVS:

NC_000009.12:g.95107205T>C
NG_011707.1:g.215505A>G
NG_027833.2:g.385508T>C
NM_000136.3:c.1394A>GMANE SELECT
NM_001243743.2:c.1394A>G
NP_000127.2:p.Gln465Arg
NP_000127.2:p.Gln465Arg
NP_001230672.1:p.Gln465Arg
LRG_497t1:c.1394A>G
LRG_497:g.215505A>G
LRG_497p1:p.Gln465Arg
NC_000009.11:g.97869487T>C
NM_000136.2:c.1394A>G
NM_001243744.1:c.*3991A>G
Q00597:p.Gln465Arg

Protein change:

Q465R

Links:

UniProtKB: Q00597#VAR_005231; dbSNP: rs1800368

NCBI 1000 Genomes Browser:

rs1800368

Molecular consequence:

NM_000136.3:c.1394A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001243743.2:c.1394A>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000695425	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Apr 29, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001365338	Leiden Open Variation Database	no assertion criteria provided	Uncertain significance (Feb 28, 2020)	germline	curation	PubMed (1) [See all records that cite this PMID]
SCV005222433	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000695425

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Apr 29, 2016)

germline

clinical testing

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

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001365338

Leiden Open Variation Database

no assertion criteria provided

Uncertain significance
(Feb 28, 2020)

germline

curation

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

SCV005222433

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign

germline

not provided

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	yes	not provided	not provided	not provided	not provided	not provided	not provided, curation
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Novel mutations and polymorphisms in the Fanconi anemia group C gene.

Gibson RA, Morgan NV, Goldstein LH, Pearson IC, Kesterton IP, Foot NJ, Jansen S, Havenga C, Pearson T, de Ravel TJ, Cohn RJ, Marques IM, Dokal I, Roberts I, Marsh J, Ball S, Milner RD, Llerena JC Jr, Samochatova E, Mohan SP, Vasudevan P, Birjandi F, et al.

Hum Mutat. 1996;8(2):140-8.

PubMed [citation]

PMID:: 8844212

Novel mutations and polymorphisms in the Fanconi anemia group C gene.

Hum Mutat. 1996;8(2):140-8.

PubMed [citation]

PMID:: 8844212

See all PubMed Citations (3)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695425.1

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

Description

Variant summary: The c.1394A>G variant affects a non-conserved nucleotide, resulting in amino acid change from Gln to Arg. 5/5 in-silico tools predict benign outcome for this variant. This variant is found in 120/120326 control chromosomes at a frequency of 0.0009973, predominantly observed in African subpopulation in ExAC with observed MAF of 1%. This frequency exceeds the maximal expected frequency of a pathogenic allele (0.0017678), suggesting this variant is likely a benign polymorphism especially for Africans. This variant has been reported in the literature (Gibson_1996) in both cohorts of affected and control individuals and was classified by authors as a polymorphism. One patients unaffected parent who was obligated heterozygous carrier was genotyped to be homozygote for this variant, further supporting the neutral effect of this variant. In addition, multiple clinical laboratory/reputable database classified this variant as benign/likely benign, without evidence to independently evaluate. Taken together, the variant was classified as Benign.

#	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 Leiden Open Variation Database, SCV001365338.1

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

Description

Curator: Arleen D. Auerbach. Submitter to LOVD: Arleen D. Auerbach.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005222433.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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