rs398123159

Positions:

• chr1-241504130-A-T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1 PP3_Strong PP5_Very_Strong

The NM_000143.4(FH):​c.1020T>A​(p.Asn340Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. N340N) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000068 (0 hom.)
• Consequence: FH NM_000143.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:10
• Conservation: PhyloP100: 0.550

Genes affected

FH (HGNC:3700): (fumarate hydratase) The protein encoded by this gene is an enzymatic component of the tricarboxylic acid (TCA) cycle, or Krebs cycle, and catalyzes the formation of L-malate from fumarate. It exists in both a cytosolic form and an N-terminal extended form, differing only in the translation start site used. The N-terminal extended form is targeted to the mitochondrion, where the removal of the extension generates the same form as in the cytoplasm. It is similar to some thermostable class II fumarases and functions as a homotetramer. Mutations in this gene can cause fumarase deficiency and lead to progressive encephalopathy. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PM1: In a hotspot region, there are 8 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 11 uncertain in NM_000143.4
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.983
• PP5: Variant 1-241504130-A-T is Pathogenic according to our data. Variant chr1-241504130-A-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 92447.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FH	NM_000143.4	c.1020T>A	p.Asn340Lys	missense_variant	7/10	ENST00000366560.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FH	ENST00000366560.4	c.1020T>A	p.Asn340Lys	missense_variant	7/10	1	NM_000143.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.0000119 AC: 3 AN: 251316 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135824

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000176

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.00000684 AC: 10 AN: 1461820 Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4 AN XY: 727216

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000899

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000868 Hom.: 0

Bravo AF: 0.0000113

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:10

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:4

Likely pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Aug 19, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Nov 23, 2021	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) -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 06, 2024	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Dec 30, 2022	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. -

Hereditary leiomyomatosis and renal cell cancer Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Jul 06, 2023	This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 31831373, 31162287, 24441663, 15937070]. -
Pathogenic, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	Jan 17, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 31, 2023	Variant summary: FH c.1020T>A (p.Asn340Lys) results in a non-conservative amino acid change located in the N-terminal Fumarate lyase domain (IPR022761) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 251316 control chromosomes. c.1020T>A has been reported in the literature in multiple individuals affected with Hereditary Leiomyomatosis And Renal Cell Cancer (example, Kamihara_2021, Truong_2021, Forde_2020, Joseph_2015, Wei_FH_JMG_2006, Toro_FH_AJHG_2003). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 31831373, 26457356, 34994643, 12772087, 34654685, 15937070). Five submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Fumarase deficiency Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Mar 02, 2024

- -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 26, 2023

The p.N340K variant (also known as c.1020T>A), located in coding exon 7 of the FH gene, results from a T to A substitution at nucleotide position 1020. The asparagine at codon 340 is replaced by lysine, an amino acid with similar properties. This alteration, referred to as N297K or N297D in some literature, has been detected in multiple HLRCC families (Ambry internal data; Wei MH et al. J Med Genet. 2006 Jan;43(1):18-27; Toro JR et al. Am J Hum Genet. 2003 Jul;73(1):95-106; Picaud S et al. J Inherit Metab Dis. 2011 Jun;34(3):671-6). This alteration has also been reported as a pathogenic mutation in a 24 year old woman from a cohort of 2060 women with uterine smooth muscle tumors (Rabban JT et al. Am J Surg Pathol, 2019 05;43:639-655). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Further, based on internal structural analysis, this variant is anticipated to result in a decrease in protein function (Ambry Internal Data; Picaud S et al. J Inherit Metab Dis. 2011 Jun;34(3):671-6). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

FH-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

May 12, 2023

The FH c.1020T>A variant is predicted to result in the amino acid substitution p.Asn340Lys. This variant has previously been reported to be causative for hereditary leiomyomatosis and renal cell cancer in several individuals (Toro et al. 2003. PubMed ID: 12772087, HGMD/ClinVar listed as T891A; Wei et al. 2006. PubMed ID: 15937070, reported as c.891T>A (N297K); Joseph et al. 2015. PubMed ID: 26457356, reported as c.1020T>A, p.N340K; Rabban JT et al 2019. PubMed ID: 30741757). This variant is reported in 0.0018% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-241667430-A-T) and is interpreted as likely pathogenic/pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/92447/?new_evidence=true). This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.20	D
BayesDel_noAF	Uncertain	0.11
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.98	D
Eigen	Uncertain	0.63
Eigen_PC	Uncertain	0.51
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Pathogenic	0.99	D
M_CAP	Pathogenic	0.93	D
MetaRNN	Pathogenic	0.98	D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	4.4	H
MutationTaster	Benign	1.0	D
PrimateAI	Pathogenic	0.82	D
PROVEAN	Pathogenic	-6.0	D
REVEL	Pathogenic	0.89
Sift	Uncertain	0.0010	D
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		1.0
MutPred		0.83		Gain of MoRF binding (P = 0.0281);
MVP		0.98
MPC		1.1
ClinPred		1.0	D
GERP RS		3.4
Varity_R		0.95
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs398123159; hg19: chr1-241667430;