NM_000143.4(FH):c.1020T>A (p.Asn340Lys) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:: Jan 6, 2024
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:: RCV000078140.27

Allele description [Variation Report for NM_000143.4(FH):c.1020T>A (p.Asn340Lys)]

NM_000143.4(FH):c.1020T>A (p.Asn340Lys)

Gene:

FH:fumarate hydratase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q43

Genomic location:

Preferred name:

NM_000143.4(FH):c.1020T>A (p.Asn340Lys)

Other names:

p.N340K:AAT>AAA

HGVS:

NC_000001.11:g.241504130A>T
NG_012338.1:g.20625T>A
NM_000143.4:c.1020T>AMANE SELECT
NP_000134.2:p.Asn340Lys
NP_000134.2:p.Asn340Lys
LRG_504t1:c.1020T>A
LRG_504:g.20625T>A
LRG_504p1:p.Asn340Lys
NC_000001.10:g.241667430A>T
NM_000143.3:c.1020T>A
p.[Asn340Lys]

Links:

dbSNP: rs398123159

NCBI 1000 Genomes Browser:

rs398123159

Molecular consequence:

NM_000143.4:c.1020T>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000109978	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Likely pathogenic (Aug 19, 2018)	germline	clinical testing	Citation Link,
SCV000251426	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Nov 23, 2021)	germline	clinical testing	Citation Link,
SCV000283659	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 6, 2024)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 12772087, 15937070, 26457356, 28492532
SCV004218857	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Pathogenic (Dec 30, 2022)	unknown	clinical testing	PubMed (7) [See all records that cite these PMIDs] 30741757, 24441663, 21445611, 16597677, 15937070, 12772087, 26467025

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	clinical testing
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

Morphology and Immunohistochemistry for 2SC and FH Aid in Detection of Fumarate Hydratase Gene Aberrations in Uterine Leiomyomas From Young Patients.

Joseph NM, Solomon DA, Frizzell N, Rabban JT, Zaloudek C, Garg K.

Am J Surg Pathol. 2015 Nov;39(11):1529-39. doi: 10.1097/PAS.0000000000000520.

PubMed [citation]

PMID:: 26457356

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

See all PubMed Citations (9)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000109978.8

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

From GeneDx, SCV000251426.13

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

Description

Not observed at a significant frequency in large population cohorts (Lek 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24684806, 21398687, 12772087, 23757202, 18366737, 28748451, 19939761, 28171700, 21445611, 24441663, 16597677, 26457356, 15937070, 31162287, 30741757)

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000283659.10

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 340 of the FH protein (p.Asn340Lys). This variant is present in population databases (rs398123159, gnomAD 0.003%). This missense change has been observed in individuals with hereditary leiomyomatosis and renal cell cancer (HLRCC) (PMID: 12772087, 15937070, 26457356; Invitae). It has also been observed to segregate with disease in related individuals. This variant is also known as 891T>A (N297K, N297D). ClinVar contains an entry for this variant (Variation ID: 92447). 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 expected to disrupt FH protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

#	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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004218857.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

The FH c.1020T>A (p.Asn340Lys) variant (also known as 891T>A, N297K or N297D) has been reported in individuals with uterine fibroid/tumor (PMID: 30741757 (2019)) and HLRCC (PMIDs: 24441663 (2014), 16597677 (2006), 15937070 (2006), 12772087 (2003)). A cell line study indicated the variant caused significantly reduced FH enzyme activity in vitro (PMID: 16597677 (2006)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function also yielded predictions that this variant is damaging. The frequency of this variant in the general population, 0.000012 (3/251316 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. Based on the available information, this variant is classified as pathogenic.

#	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

Last Updated: Oct 26, 2024

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