ClinVar Genomic variation as it relates to human health
NM_213653.4(HJV):c.959G>T (p.Gly320Val)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_213653.4(HJV):c.959G>T (p.Gly320Val)
Variation ID: 2365 Accession: VCV000002365.50
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 1q21.1 1: 146018399 (GRCh38) [ NCBI UCSC ] 1: 145416614 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 26, 2015 Oct 20, 2024 Jul 31, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_213653.4:c.959G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_998818.1:p.Gly320Val missense NM_001316767.2:c.281G>T NP_001303696.1:p.Gly94Val missense NM_001379352.1:c.959G>T NP_001366281.1:p.Gly320Val missense NM_145277.5:c.620G>T NP_660320.3:p.Gly207Val missense NM_202004.4:c.281G>T NP_973733.1:p.Gly94Val missense NM_213652.4:c.281G>T NP_998817.1:p.Gly94Val missense NC_000001.11:g.146018399C>A NC_000001.10:g.145416614G>T NG_011568.1:g.8424G>T Q6ZVN8:p.Gly320Val - Protein change
- G320V, G207V, G94V
- Other names
- -
- Canonical SPDI
- NC_000001.11:146018398:C:A
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
Exome Aggregation Consortium (ExAC) 0.00017
The Genome Aggregation Database (gnomAD), exomes 0.00017
The Genome Aggregation Database (gnomAD) 0.00027
Trans-Omics for Precision Medicine (TOPMed) 0.00028
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
HJV | - | - |
GRCh38 GRCh37 |
387 | 574 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
Pathogenic (5) |
criteria provided, multiple submitters, no conflicts
|
Jul 31, 2024 | RCV000002461.20 | |
Pathogenic (1) |
no assertion criteria provided
|
Nov 1, 2009 | RCV000002462.5 | |
Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
|
Feb 1, 2024 | RCV000791424.32 | |
Pathogenic (1) |
criteria provided, single submitter
|
Mar 28, 2018 | RCV004017220.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
---|---|---|---|---|---|
Pathogenic
(May 11, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV002601489.2
First in ClinVar: Nov 19, 2022 Last updated: Mar 04, 2023 |
Comment:
Published functional studies demonstrate a damaging effect (Pagani et al., 2008; Silvestri et al., 2007; Zhang et al., 2005); In silico analysis supports that this … (more)
Published functional studies demonstrate a damaging effect (Pagani et al., 2008; Silvestri et al., 2007; Zhang et al., 2005); 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: 15967692, 27753142, 14982867, 20234129, 15811010, 20593054, 32189932, 23651750, 17339196, 19796184, 31640930, 30389309, 15254010, 30362946, 29373985, 22408404, 15610558, 14982873, 12891378, 17264300, 16103117, 18827264, 26142323, 14647275) (less)
|
|
Pathogenic
(Oct 15, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Hemochromatosis type 2A
Affected status: unknown
Allele origin:
germline
|
Revvity Omics, Revvity
Accession: SCV002024998.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
|
|
Pathogenic
(Jan 25, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000546647.8
First in ClinVar: Feb 05, 2017 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 320 of the HJV protein (p.Gly320Val). … (more)
This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 320 of the HJV protein (p.Gly320Val). This variant is present in population databases (rs74315323, gnomAD 0.04%). This missense change has been observed in individual(s) with juvenile hemochromatosis (PMID: 14647275, 14982873, 15811010, 22408404). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 2365). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects HJV function (PMID: 16103117, 18827264). For these reasons, this variant has been classified as Pathogenic. (less)
|
|
Pathogenic
(Mar 28, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Juvenile hemochromatosis
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
|
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Study: CSER-MedSeq
Accession: SCV000221191.3 First in ClinVar: Apr 01, 2015 Last updated: Apr 20, 2024 |
Comment:
The Gly320Val variant in HFE2 is the most frequent pathogenic variant in HFE2 (also known as HJV) and has been reported in many patients with … (more)
The Gly320Val variant in HFE2 is the most frequent pathogenic variant in HFE2 (also known as HJV) and has been reported in many patients with juvenile hemochromatosis, both in the homozygous and compound heterozygous states (Papanikolaou 2004, Lanzara 2004, Lee 2004, Agilar-Martinez 2007). It has been identified in 0.04% (4/8600) of European American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/; dbSNP rs74315323). In summary, this variant meets our criteria to be classified as pathogenic (http://pcpgm.partners.org/LMM). (less)
|
|
Pathogenic
(Feb 01, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Clinical Genetics Laboratory, Skane University Hospital Lund
Accession: SCV005198440.1
First in ClinVar: Aug 25, 2024 Last updated: Aug 25, 2024 |
|
|
Pathogenic
(Dec 19, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Hemochromatosis type 2A
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000915351.1
First in ClinVar: May 27, 2019 Last updated: May 27, 2019 |
Comment:
Across a selection of the available literature, the HEF2 c.959G>T (p.Gly320Val) missense variant, described as the most common variant associated with juvenile hereditary hemochromatosis, has … (more)
Across a selection of the available literature, the HEF2 c.959G>T (p.Gly320Val) missense variant, described as the most common variant associated with juvenile hereditary hemochromatosis, has been identified in a homozygous state in at least 30 individuals with juvenile hereditary hemochromatosis and in a compound heterozygous state in another four individuals (Papanikolaou et al. 2004; Lanzara et al. 2004; Gehrke et al. 2005; Aguilar-Martinez et al. 2007; Brakensiek et al 2009; Farrell et al. 2015). The p.Gly320Val variant was absent from over 900 controls including approximately 360 healthy Caucasian and African American individuals, and is reported at a frequency of 0.00047 in the European American population of the Exome Sequencing Project (Papanikolaou et al. 20This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.04; Lanzara et al. 2004; Barton et al. 2004). The Gly320 residue is highly conserved across species (Papanikolaou et al. 2004). Based on the collective evidence, the p.Gly320Val variant is classified as pathogenic for juvenile hereditary hemochromatosis. The GJA5 c.744C>A (p.Cys248Ter) variant is a stop gained variant predicted to result in premature termination of the protein. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. This variant is not found in the 1000 Genomes Project, the Exome Sequencing Project, Exome Aggregation Consortium, or the Genome Aggregation Database. This variant is located in the last exon and may escape nonsense-mediated decay. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of stop-gained variants and the lack of clarifying evidence, the p.Cys248Ter variant is classified as a variant of unknown significance but suspicious for pathogenicity for familial atrial fibrillation. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. (less)
|
|
Pathogenic
(Jul 31, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Hemochromatosis type 2A
Affected status: unknown
Allele origin:
germline
|
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV005202278.1
First in ClinVar: Sep 16, 2024 Last updated: Sep 16, 2024 |
Comment:
Variant summary: HJV c.959G>T (p.Gly320Val) results in a non-conservative amino acid change located in the Repulsive guidance molecule, C-terminal domain (IPR009496) of the encoded protein … (more)
Variant summary: HJV c.959G>T (p.Gly320Val) results in a non-conservative amino acid change located in the Repulsive guidance molecule, C-terminal domain (IPR009496) of the encoded protein sequence. Four of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00042 in 1614004 control chromosomes in the gnomAD database, including 1 homozygotes. This frequency is not significantly higher than estimated for a pathogenic variant in HJV causing Hemochromatosis Type 2A (0.00042 vs 0.0011), allowing no conclusion about variant significance. c.959G>T has been reported in the literature in multiple individuals affected with Hemochromatosis (example: Papanikolaou_2004). These data indicate that the variant is very likely to be associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 14647275). ClinVar contains an entry for this variant (Variation ID: 2365). Based on the evidence outlined above, the variant was classified as pathogenic. (less)
|
|
Pathogenic
(Feb 01, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
CeGaT Center for Human Genetics Tuebingen
Accession: SCV001249628.26
First in ClinVar: May 09, 2020 Last updated: Oct 20, 2024 |
Number of individuals with the variant: 1
|
|
Pathogenic
(Nov 01, 2009)
|
no assertion criteria provided
Method: literature only
|
HEMOCHROMATOSIS, TYPE 2A
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000022619.3
First in ClinVar: Apr 04, 2013 Last updated: Feb 05, 2017 |
Comment on evidence:
In 7 of 10 Greek families with juvenile hemochromatosis (HFE2A; 602390), Papanikolaou et al. (2004) identified a homozygous gly320-to-val (G320V) mutation in the HJV gene. … (more)
In 7 of 10 Greek families with juvenile hemochromatosis (HFE2A; 602390), Papanikolaou et al. (2004) identified a homozygous gly320-to-val (G320V) mutation in the HJV gene. Affected individuals shared the common Greek haplotype. This same mutation was found in 1 Canadian and 1 French family with juvenile hemochromatosis. In 1 Greek family, the G320V mutation was in compound heterozygous state with arg326 to ter (R326X; 608374.0002), and in 1 Canadian family, G320V was in compound heterozygous state with ile222 to asn (I222N; 608374.0003). In a white female diagnosed with hereditary hemochromatosis (HFE1; 235200) at the age of 30 years when she presented with progressive fatigue and early onset of menopause, Lee et al. (2004) identified compound heterozygosity for mutations in the HJV gene: G320V and cys321 to trp (C321W; 608374.0007). Pituitary insufficiency was diagnosed, and deeply pigmented skin, elevated serum iron, and total iron binding capacity, as well as transferrin saturation, were found. The patient had had 2 normal pregnancies, the last when she was 21 years old; she developed amenorrhea at age 23 years. Her medical history also included hypothyroidism treated with thyroxine for most of her adult life. She also had had multiple dental problems since early adulthood, requiring a dental implant. She developed type II diabetes (125853) at age 59 years, which was controlled by an oral hypoglycemic agent. In 17 patients with juvenile hemochromatosis (JH) from 12 families of the isolated region of Saguenay-Lac-Saint-Jean in Quebec, who were previously studied by Rivard et al. (2003), Lanzara et al. (2004) identified homozygosity for the G320V mutation. However, among 13 unrelated Italian JH patients in the study, the only G320V homozygote was likely of Greek ancestry, because he lived in a southern Italian region where a dialect resembling Greek was still spoken. In 6 of 7 patients with JH from 6 unrelated central European families (from Germany, Slovakia, and Croatia), Gehrke et al. (2005) identified homozygosity for the G320V mutation in 4 patients and compound heterozygosity for G320V and a 4-bp deletion (608374.0008) in 2 patients. Gehrke et al. (2005) concluded that the genetic background of JH might be more homogeneous than initially believed. In a Croatian patient who had the most severe phenotype, with liver cirrhosis, severe dilated cardiomyopathy, and hypogonadism, Gehrke et al. (2005) also found a heterozygous C282Y mutation in the HFE gene (613609.0001) and suggested that HFE mutations might influence the phenotypic expression in HJV-related JH. In a 21-year-old male patient with hemochromatosis who died due to low cardiac output and multiorgan failure, Brakensiek et al. (2009) identified homozygosity for the G320V mutation in the HJV gene, as well as compound heterozygosity for the H63D (613609.0002) and S65C (613609.0003) mutations in the HFE gene. Brakensiek et al. (2009) suggested that severity of the clinical course in this patient might be related to the complex genotype. (less)
|
|
Pathogenic
(Nov 01, 2009)
|
no assertion criteria provided
Method: literature only
|
HEMOCHROMATOSIS, HEREDITARY
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000022620.3
First in ClinVar: Apr 04, 2013 Last updated: Feb 05, 2017 |
Comment on evidence:
In 7 of 10 Greek families with juvenile hemochromatosis (HFE2A; 602390), Papanikolaou et al. (2004) identified a homozygous gly320-to-val (G320V) mutation in the HJV gene. … (more)
In 7 of 10 Greek families with juvenile hemochromatosis (HFE2A; 602390), Papanikolaou et al. (2004) identified a homozygous gly320-to-val (G320V) mutation in the HJV gene. Affected individuals shared the common Greek haplotype. This same mutation was found in 1 Canadian and 1 French family with juvenile hemochromatosis. In 1 Greek family, the G320V mutation was in compound heterozygous state with arg326 to ter (R326X; 608374.0002), and in 1 Canadian family, G320V was in compound heterozygous state with ile222 to asn (I222N; 608374.0003). In a white female diagnosed with hereditary hemochromatosis (HFE1; 235200) at the age of 30 years when she presented with progressive fatigue and early onset of menopause, Lee et al. (2004) identified compound heterozygosity for mutations in the HJV gene: G320V and cys321 to trp (C321W; 608374.0007). Pituitary insufficiency was diagnosed, and deeply pigmented skin, elevated serum iron, and total iron binding capacity, as well as transferrin saturation, were found. The patient had had 2 normal pregnancies, the last when she was 21 years old; she developed amenorrhea at age 23 years. Her medical history also included hypothyroidism treated with thyroxine for most of her adult life. She also had had multiple dental problems since early adulthood, requiring a dental implant. She developed type II diabetes (125853) at age 59 years, which was controlled by an oral hypoglycemic agent. In 17 patients with juvenile hemochromatosis (JH) from 12 families of the isolated region of Saguenay-Lac-Saint-Jean in Quebec, who were previously studied by Rivard et al. (2003), Lanzara et al. (2004) identified homozygosity for the G320V mutation. However, among 13 unrelated Italian JH patients in the study, the only G320V homozygote was likely of Greek ancestry, because he lived in a southern Italian region where a dialect resembling Greek was still spoken. In 6 of 7 patients with JH from 6 unrelated central European families (from Germany, Slovakia, and Croatia), Gehrke et al. (2005) identified homozygosity for the G320V mutation in 4 patients and compound heterozygosity for G320V and a 4-bp deletion (608374.0008) in 2 patients. Gehrke et al. (2005) concluded that the genetic background of JH might be more homogeneous than initially believed. In a Croatian patient who had the most severe phenotype, with liver cirrhosis, severe dilated cardiomyopathy, and hypogonadism, Gehrke et al. (2005) also found a heterozygous C282Y mutation in the HFE gene (613609.0001) and suggested that HFE mutations might influence the phenotypic expression in HJV-related JH. In a 21-year-old male patient with hemochromatosis who died due to low cardiac output and multiorgan failure, Brakensiek et al. (2009) identified homozygosity for the G320V mutation in the HJV gene, as well as compound heterozygosity for the H63D (613609.0002) and S65C (613609.0003) mutations in the HFE gene. Brakensiek et al. (2009) suggested that severity of the clinical course in this patient might be related to the complex genotype. (less)
|
|
Pathogenic
(Jan 11, 2020)
|
no assertion criteria provided
Method: clinical testing
|
Hemochromatosis type 2A
Affected status: unknown
Allele origin:
germline
|
Natera, Inc.
Accession: SCV002085767.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022 |
|
|
click to load more click to collapse |
Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
Molecular diagnostic and pathogenesis of hereditary hemochromatosis. | Santos PCJL | International journal of molecular sciences | 2012 | PMID: 22408404 |
Juvenile hemochromatosis due to homozygosity for the G320V mutation in the HJV gene with fatal outcome. | Brakensiek K | Clinical genetics | 2009 | PMID: 19796184 |
Hemojuvelin N-terminal mutants reach the plasma membrane but do not activate the hepcidin response. | Pagani A | Haematologica | 2008 | PMID: 18827264 |
Juvenile hemochromatosis caused by a novel combination of hemojuvelin G320V/R176C mutations in a 5-year old girl. | Aguilar-Martinez P | Haematologica | 2007 | PMID: 17339196 |
Interaction of hemojuvelin with neogenin results in iron accumulation in human embryonic kidney 293 cells. | Zhang AS | The Journal of biological chemistry | 2005 | PMID: 16103117 |
HJV gene mutations in European patients with juvenile hemochromatosis. | Gehrke SG | Clinical genetics | 2005 | PMID: 15811010 |
Allele frequencies of hemojuvelin gene (HJV) I222N and G320V missense mutations in white and African American subjects from the general Alabama population. | Barton JC | BMC medical genetics | 2004 | PMID: 15610558 |
The recently identified type 2A juvenile haemochromatosis gene (HJV), a second candidate modifier of the C282Y homozygous phenotype. | Le Gac G | Human molecular genetics | 2004 | PMID: 15254010 |
Spectrum of hemojuvelin gene mutations in 1q-linked juvenile hemochromatosis. | Lanzara C | Blood | 2004 | PMID: 14982873 |
Genetic abnormalities and juvenile hemochromatosis: mutations of the HJV gene encoding hemojuvelin. | Lee PL | Blood | 2004 | PMID: 14982867 |
Mutations in HFE2 cause iron overload in chromosome 1q-linked juvenile hemochromatosis. | Papanikolaou G | Nature genetics | 2004 | PMID: 14647275 |
Juvenile hemochromatosis locus maps to chromosome 1q in a French Canadian population. | Rivard SR | European journal of human genetics : EJHG | 2003 | PMID: 12891378 |
click to load more click to collapse |
Text-mined citations for rs74315323 ...
HelpRecord last updated Oct 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.