U.S. flag

An official website of the United States government

NM_000410.4(HFE):c.193A>T (p.Ser65Cys) AND Hemochromatosis type 1

Germline classification:
Conflicting interpretations of pathogenicity (6 submissions)
Last evaluated:
Jul 17, 2023
Review status:
criteria provided, conflicting classifications
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:
RCV000000028.25

Allele description [Variation Report for NM_000410.4(HFE):c.193A>T (p.Ser65Cys)]

NM_000410.4(HFE):c.193A>T (p.Ser65Cys)

Genes:
HFE-AS1:HFE antisense RNA 1 [Gene - HGNC]
HFE:homeostatic iron regulator [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p22.2
Genomic location:
Preferred name:
NM_000410.4(HFE):c.193A>T (p.Ser65Cys)
HGVS:
  • NC_000006.12:g.26090957A>T
  • NG_008720.2:g.8677A>T
  • NM_000410.4:c.193A>TMANE SELECT
  • NM_001300749.3:c.193A>T
  • NM_001384164.1:c.193A>T
  • NM_001406751.1:c.193A>T
  • NM_139003.3:c.193A>T
  • NM_139004.3:c.193A>T
  • NM_139006.3:c.193A>T
  • NM_139007.3:c.77-357A>T
  • NM_139008.3:c.77-357A>T
  • NM_139009.3:c.124A>T
  • NM_139010.3:c.77-1728A>T
  • NM_139011.3:c.77-2162A>T
  • NP_000401.1:p.Ser65Cys
  • NP_000401.1:p.Ser65Cys
  • NP_000401.1:p.Ser65Cys
  • NP_001287678.1:p.Ser65Cys
  • NP_001287678.1:p.Ser65Cys
  • NP_001371093.1:p.Ser65Cys
  • NP_001393680.1:p.Ser65Cys
  • NP_620572.1:p.Ser65Cys
  • NP_620573.1:p.Ser65Cys
  • NP_620575.1:p.Ser65Cys
  • NP_620578.1:p.Ser42Cys
  • LRG_748t1:c.193A>T
  • LRG_748:g.8677A>T
  • LRG_748p1:p.Ser65Cys
  • NC_000006.11:g.26091185A>T
  • NM_000410.3:c.193A>T
  • NM_001300749.2:c.193A>T
  • NR_144383.1:n.78T>A
  • Q30201:p.Ser65Cys
Protein change:
S42C; SER65CYS
Links:
Genetic Testing Registry (GTR): GTR000321635; UniProtKB: Q30201#VAR_004397; OMIM: 613609.0003; dbSNP: rs1800730
NCBI 1000 Genomes Browser:
rs1800730
Molecular consequence:
  • NM_139007.3:c.77-357A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_139008.3:c.77-357A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_139010.3:c.77-1728A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_139011.3:c.77-2162A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000410.4:c.193A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001300749.3:c.193A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384164.1:c.193A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406751.1:c.193A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_139003.3:c.193A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_139004.3:c.193A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_139006.3:c.193A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_139009.3:c.124A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_144383.1:n.78T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Hemochromatosis type 1 (HFE1)
Synonyms:
HFE-Associated Hereditary Hemochromatosis
Identifiers:
MONDO: MONDO:0021001; MedGen: C3469186; OMIM: 235200

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000020171OMIM
no assertion criteria provided
Pathogenic
(Apr 15, 1999)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000206974Blueprint Genetics
no assertion criteria provided
Pathogenic
(Nov 11, 2014)
germlineclinical testing

SCV000245790GeneReviews
no classification provided
not providedgermlineliterature only

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

SCV000461884Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)
Uncertain significance
(Jul 27, 2017)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Citation Link,

SCV002044432Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Dec 7, 2021)
unknownclinical testing

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

SCV005086727Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(Jul 17, 2023)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, literature only
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Diagnosis of hemochromatosis in family members of probands: a comparison of phenotyping and HFE genotyping.

Barton JC, Rothenberg BE, Bertoli LF, Acton RT.

Genet Med. 1999 Mar-Apr;1(3):89-93.

PubMed [citation]
PMID:
11336458

Effects of C282Y, H63D, and S65C HFE gene mutations, diet, and life-style factors on iron status in a general Mediterranean population from Tarragona, Spain.

Aranda N, Viteri FE, Montserrat C, Arija V.

Ann Hematol. 2010 Aug;89(8):767-73. doi: 10.1007/s00277-010-0901-9. Epub 2010 Jan 28.

PubMed [citation]
PMID:
20107990
PMCID:
PMC2887936
See all PubMed Citations (10)

Details of each submission

From OMIM, SCV000020171.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

Mura et al. (1999) reported on the analysis of the cys282-to-tyr (C282Y; 613609.0001), his63-to-asp (H63D; 613609.0002), and ser65-to-cys (S65C) mutations of the HFE gene in a series of 711 probands with hereditary hemochromatosis (235200) and 410 controls. The results confirmed that the C282Y substitution is the main mutation involved in HH, accounting for 85% of carrier chromosomes, whereas the H63D substitution represented 39% of the HH chromosomes that did not carry the C282Y mutation. In addition, the screening showed that the S65C substitution, which results from a 193A-T transversion, was significantly enriched in probands with at least 1 chromosome without an assigned mutation. This substitution accounted for 7.8% of HH chromosomes that were neither C282Y nor H63D. This enrichment of S65C among HH chromosomes suggested that the S65C substitution is associated with a mild form of hemochromatosis.

Barton et al. (1999) identified the S65C mutation in 2 patients. One was also heterozygous for C282Y, i.e., was a compound heterozygote, and had porphyria cutanea tarda (see 176100). The other patient had hereditary stomatocytosis (185000). Iron overload due to the HFE mutations probably precipitated or exacerbated the porphyria cutanea tarda in the first patient. In the second patient, iron overload from the hereditary stomatocytosis undoubtedly exacerbated the iron overload due to the HFE mutation.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Blueprint Genetics, SCV000206974.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From GeneReviews, SCV000245790.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV000461884.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

The HFE c.193A>T (p.Ser65Cys) variant is a missense variant that has been reported to be enriched in individuals affected with hereditary hemochromatosis as compared to unaffected individuals in two studies (Mura et al. 1999; Holmstrom et al. 2002). The authors suggested that the p.Ser65Cys variant is associated with a mild phenotype, resulting in a lower degree of iron overload as compared to common pathogenic variants in the HFE gene. Two functional studies have reported that the p.Ser65Cys variant alone has no significant influence on iron status markers (Pedersen et al. 2009; Aranda et al. 2010), and Bacon et al. (2011) and Alves et al. (2016) discuss that the p.Ser65Cys variant is generally not associated with iron loading unless seen in a compound heterozygous state with either the p.Cys282Tyr or p.His63Asp variant. The p.Ser65Cys variant is reported at a frequency of 0.03846 in the British of England and Scotland population of the 1000 Genomes Project, which is consistent with estimates of disease prevalence and penetrance. Although p.Ser65Cys variant is widely reported in the literature as the third most common variant associated with HFE-related hereditary hemochromatosis (Seckington et al. 2015), the functional evidence suggests that this variant may not contribute to the mechanism of disease. Based on this conflicting evidence, the p.Ser65Cys is classified as a variant of unknown significance but suspicious for pathogenicity for hereditary hemochromatosis. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV002044432.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

_x000D_This variant was identified as compound heterozygous with NM_000410.4:c.845G>A. Criteria applied: PM3, PP3, BS3_SUP

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV005086727.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Based on the classification scheme VCGS_Germline_v1.3.3, this variant is classified as Likely benign. Following criteria are met: 0805 - This variant has strong previous evidence of being benign in unrelated individuals. The EMQN practice guidelines state that there is no evidence to support a causative role of this variant in hereditary haemochromatosis (PMID: 26153218). (SB) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 16, 2024