NM_004629.2(FANCG):c.890C>T (p.Thr297Ile) AND Fanconi anemia complementation group G

Germline classification:: Benign (4 submissions)
Last evaluated:: Jul 7, 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:: RCV001166139.7

Allele description [Variation Report for NM_004629.2(FANCG):c.890C>T (p.Thr297Ile)]

NM_004629.2(FANCG):c.890C>T (p.Thr297Ile)

Genes:

VCP:valosin containing protein [Gene - OMIM - HGNC]
FANCG:FA complementation group G [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9p13.3

Genomic location:

Preferred name:

NM_004629.2(FANCG):c.890C>T (p.Thr297Ile)

HGVS:

NC_000009.12:g.35076758G>A
NG_007312.1:g.8259C>T
NG_007887.1:g.985C>T
NM_004629.2:c.890C>TMANE SELECT
NP_004620.1:p.Thr297Ile
NP_004620.1:p.Thr297Ile
LRG_499t1:c.890C>T
LRG_499:g.8259C>T
LRG_499p1:p.Thr297Ile
LRG_657:g.985C>T
NC_000009.11:g.35076755G>A
NM_004629.1:c.890C>T
O15287:p.Thr297Ile

Protein change:

T297I

Links:

UniProtKB: O15287#VAR_020311; dbSNP: rs2237857

NCBI 1000 Genomes Browser:

rs2237857

Molecular consequence:

NM_004629.2:c.890C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Fanconi anemia complementation group G
Synonyms:: Fanconi anemia group G
Identifiers:: MONDO: MONDO:0013565; MedGen: C3469527; Orphanet: 84; OMIM: 614082

Recent activity

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Brucella suis 1330 chromosome I, complete sequence
Brucella suis 1330 chromosome I, complete sequence
gi|384223698|ref|NC_017251.1|

Nucleotide
605991 (1)
OMIM
607870 (1)
OMIM
Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/VA-...
Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/VA-DCLS-0075/2020, complete genome
gi|1836048771|gb|MT415899.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001328479	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Mar 6, 2018)	germline	clinical testing	Citation Link,
SCV001364822	Leiden Open Variation Database	no assertion criteria provided	Pathogenic (Feb 7, 2011)	germline	curation	PubMed (1) [See all records that cite this PMID]
SCV001452305	Natera, Inc.	no assertion criteria provided	Benign (Sep 16, 2020)	germline	clinical testing
SCV004017689	KCCC/NGS Laboratory, Kuwait Cancer Control Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 7, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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

Citations

PubMed

Functional analysis of patient-derived mutations in the Fanconi anemia gene, FANCG/XRCC9.

Nakanishi K, Moran A, Hays T, Kuang Y, Fox E, Garneau D, Montes de Oca R, Grompe M, D'Andrea AD.

Exp Hematol. 2001 Jul;29(7):842-9.

PubMed [citation]

PMID:: 11438206

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 Illumina Laboratory Services, Illumina, SCV001328479.1

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	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, SCV001364822.1

#	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 Natera, Inc., SCV001452305.1

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

#	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 KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004017689.1

#	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	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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