rs863224004

Variant names:

• chr1-241504053-C-T
• rs863224004
• NM_000143.4:c.1097G>A

Variant summary

Our verdict is Pathogenic. The variant received 17 ACMG points: 17P and 0B. PM1 PM2 PP2 PP3_Strong PP5_Very_Strong

The NM_000143.4(FH):​c.1097G>A​(p.Ser366Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,696 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. S366S) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: FH NM_000143.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:8
• Conservation: PhyloP100: 7.37
• Publications: 3 publications found

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]

FH Gene-Disease associations (from GenCC):

• hereditary leiomyomatosis and renal cell cancer

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Ambry Genetics, G2P, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Orphanet
• fumaric aciduria

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
• pheochromocytoma-paraganglioma

  Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics
• leiomyosarcoma

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• hereditary pheochromocytoma-paraganglioma

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 17 ACMG points.

• PM1: In a hotspot region, there are 12 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 13 uncertain in NM_000143.4
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 132 curated pathogenic missense variants (we use a threshold of 10). The gene has 17 curated benign missense variants. Gene score misZ: 1.2708 (below the threshold of 3.09). Trascript score misZ: 2.0634 (below the threshold of 3.09). GenCC associations: The gene is linked to fumaric aciduria, hereditary leiomyomatosis and renal cell cancer, hereditary pheochromocytoma-paraganglioma, leiomyosarcoma, pheochromocytoma-paraganglioma.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.948
• PP5: Variant 1-241504053-C-T is Pathogenic according to our data. Variant chr1-241504053-C-T is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 214419.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FH	NM_000143.4	c.1097G>A	p.Ser366Asn	missense_variant	Exon 7 of 10	ENST00000366560.4	NP_000134.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FH	ENST00000366560.4	c.1097G>A	p.Ser366Asn	missense_variant	Exon 7 of 10	1	NM_000143.4	ENSP00000355518.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461696 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 727136

African (AFR) AF: 0.00 AC: 0 AN: 33474

American (AMR) AF: 0.00 AC: 0 AN: 44680

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26120

East Asian (EAS) AF: 0.00 AC: 0 AN: 39696

South Asian (SAS) AF: 0.00 AC: 0 AN: 86204

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53416

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1111944

Other (OTH) AF: 0.00 AC: 0 AN: 60394

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:8

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:4

Dec 20, 2023

Mayo Clinic Laboratories, Mayo Clinic

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PP3, PP4, PP5, PM1, PM2_moderate -

Feb 20, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as FH c.968G>A, p.Ser323Asn; This variant is associated with the following publications: (PMID: 15937070, 12761039, 31299266, 18366737, 21630274, 12772087, 16597677, 16029320, 16237213, 30761759, 22561013, 35022142, 31831373, 21445611) -

Jul 22, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 366 of the FH protein (p.Ser366Asn). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with multiple cutaneous and uterine leiomyomatosis (MCUL) or hereditary leiomyomatosis and renal cell cancer (HLRCC) (PMID: 12761039, 12772087, 16237213; Invitae). This variant is also known as G968A or S323N. ClinVar contains an entry for this variant (Variation ID: 214419). 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. -

Jul 26, 2023

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The FH c.1097G>A (p.Ser366Asn) variant has been reported in the published literature in individuals with phenotypes associated with hereditary leiomyomatosis and renal cell cancer (HLRCC)(PMID: 12772087 (2003), 16237213 (2005), 21630274 (2011), 31299266 (2019)). Immunohistochemical analysis of tumors from patients with this variant showed loss of heterozygosity and were positive for (2-succinyl) cysteine (2SC) (termed protein succination) due to deficient fumarase (PMID: 21630274 (2011)). Additionally, this variant is predicted to alter the active site of the FH protein (PMID: 21445611 (2011), 12761039 (2003)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, this variant is classified as pathogenic. -

Hereditary leiomyomatosis and renal cell cancer Pathogenic:2

Oct 03, 2022

St. Jude Molecular Pathology, St. Jude Children's Research Hospital

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The FH c.1097G>A (p.Ser366Asn) missense change is absent in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). This variant has been identified in multiple individuals with leiomyomas and/or renal cell carcinoma (PMID: 12761039, 12772087, 21630274). The tumors of at least three of these individuals also demonstrated loss of heterozygosity (PMID: 12761039, 21630274). In addition, immunohistochemical analysis of tumors from patients with this germline variant have shown an accumulation of succinated proteins as a result of fumarase deficiency (PMID: 21630274). The in silico tool REVEL predicts a deleterious effect on protein function, but to our knowledge this prediction has not been confirmed by functional studies. This variant is also known as p.Ser323Asn in the literature. In summary, this variant meets criteria to be classified as likely pathogenic. -

Jan 17, 2023

Myriad Genetics, Inc.

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 12761039, 31299266, 31831373, 21630274, 12772087]. -

Fumarase deficiency Pathogenic:1

Dec 22, 2023

Baylor Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Pathogenic:1

May 23, 2023

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.S366N pathogenic mutation (also known as c.1097G>A), located in coding exon 7 of the FH gene, results from a G to A substitution at nucleotide position 1097. The serine at codon 366 is replaced by asparagine, an amino acid with highly similar properties. This alteration has been reported in numerous individuals with multiple cutaneous and uterine leiyomyomatosis (Alam NA et al. J Mol Diagn. 2005 Oct;7:437-43; Toro JR et al. Am. J. Hum. Genet. 2003 Jul;73:95-106; Bardella C et al. J. Pathol. 2011 Sep;225(1):4-11; Gupta S et al. Hum Pathol, 2019 Sep;91:114-122; Ambry internal data). Immunohistochemical analysis of tumors in patients with the germline p.S366N mutation have shown that this alteration results in an accumulation of succinated proteins as a result of deficient fumarase; these patients' tumors also demonstrated loss of heterozygosity (Bardella C et al. J. Pathol. 2011 Sep;225(1):4-11). In addition, the p.S366N variant has been predicted to alter the enzymatic active site of the FH protein (Picaud S et al. J. Inherit. Metab. Dis. 2011 Jun;34:671-6; Alam NA et al. Hum. Mol. Genet. 2003 Jun;12:1241-52). Based on internal structural analysis, this variant is anticipated to disrupt a region of known function (Ajalla Aleixo MA et al. FEBS J. 2019 May;286:1925-1940; Mechaly AE et al. FEBS Lett. 2012 Jun;586:1606-11). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Of note, this alteration is also designated as S323N (c.968G>A) in some published literature. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.21
CADD	Pathogenic	30
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.99	D
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	0.99	D
M_CAP	Pathogenic	0.83	D
MetaRNN	Pathogenic	0.95	D
MetaSVM	Pathogenic	0.93	D
MutationAssessor	Pathogenic	5.1	H
PhyloP100		7.4
PrimateAI	Pathogenic	0.82	D
PROVEAN	Uncertain	-3.0	D
REVEL	Pathogenic	0.88
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.96
MutPred		0.70		Loss of phosphorylation at S366 (P = 0.0501);
MVP		0.98
MPC		0.90
ClinPred		1.0	D
GERP RS		5.7
Varity_R		0.98
gMVP		0.98
Mutation Taster		=7/93	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs863224004; hg19: chr1-241667353;