NM_139011.3(HFE):c.77-2168C>G AND multiple conditions

replaced

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 25, 2018
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001197569.1

Allele description

NM_139011.3(HFE):c.77-2168C>G

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_139011.3(HFE):c.77-2168C>G

HGVS:

NC_000006.12:g.26090951C>G
NG_008720.2:g.8671C>G
NM_000410.3:c.187C>G
NM_000410.3:c.187C>G
NM_001300749.2:c.187C>G
NM_139003.3:c.187C>G
NM_139004.3:c.187C>G
NM_139006.3:c.187C>G
NM_139007.3:c.77-363C>G
NM_139008.3:c.77-363C>G
NM_139009.3:c.118C>G
NM_139010.3:c.77-1734C>G
NM_139011.3:c.77-2168C>G
NP_000401.1:p.His63Asp
NP_001287678.1:p.His63Asp
NP_620572.1:p.His63Asp
NP_620573.1:p.His63Asp
NP_620575.1:p.His63Asp
NP_620578.1:p.His40Asp
LRG_748t1:c.187C>G
LRG_748:g.8671C>G
LRG_748p1:p.His63Asp
NC_000006.11:g.26091179C>G
NG_008720.1:p.His63Asp
NM_139011.2:c.77-2168C>G
NR_144383.1:n.84G>C
Q30201:p.His63Asp

Protein change:

H40D; His63Asp

Links:

Genetic Testing Registry (GTR): GTR000021464; Genetic Testing Registry (GTR): GTR000509340; UniProtKB: Q30201#VAR_004396; OMIM: 613609.0002; dbSNP: rs1799945

NCBI 1000 Genomes Browser:

rs1799945

Molecular consequence:

NM_139007.3:c.77-363C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_139008.3:c.77-363C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_139010.3:c.77-1734C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_139011.3:c.77-2168C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000410.3:c.187C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001300749.2:c.187C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_139003.3:c.187C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_139004.3:c.187C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_139006.3:c.187C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_139009.3:c.118C>G - missense variant - [Sequence Ontology: SO:0001583]
NR_144383.1:n.84G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Type 2 diabetes mellitus (T2D)
Synonyms:: DIABETES MELLITUS, TYPE 2, PROTECTION AGAINST; DIABETES MELLITUS, TYPE II, SUSCEPTIBILITY TO; NIDDM diabetes mellitus; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0005148; MeSH: D003924; MedGen: C0011860; OMIM: 125853; Human Phenotype Ontology: HP:0005978

Name:: Restrictive cardiomyopathy
Identifiers:: MONDO: MONDO:0005201; MeSH: D002313; MedGen: C0007196; Human Phenotype Ontology: HP:0001723

Name:: Increased serum ferritin
Synonyms:: Elevated serum ferritin; Increased ferritin; Increased serum ferritin level; See all synonyms [MedGen]
Identifiers:: MedGen: C0241013; Human Phenotype Ontology: HP:0003281

Name:: Elevated transferrin saturation
Identifiers:: MedGen: C4022892; Human Phenotype Ontology: HP:0012463

Name:: Elevated hepatic iron concentration
Synonyms:: Increased iron concentration in liver; Increased liver iron level
Identifiers:: MedGen: C4022891; Human Phenotype Ontology: HP:0012465

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001368348	Centre for Mendelian Genomics,University Medical Centre Ljubljana	criteria provided, single submitter (ACMG guidelines, Richards 2015)	Pathogenic (Sep 25, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001368348

Centre for Mendelian Genomics,University Medical Centre Ljubljana

criteria provided, single submitter

(ACMG guidelines, Richards 2015)

Pathogenic
(Sep 25, 2018)

germline

clinical testing

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

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

Citations

PubMed

Expert specification of the ACMG/AMP variant interpretation guidelines for genetic hearing loss.

Oza AM, DiStefano MT, Hemphill SE, Cushman BJ, Grant AR, Siegert RK, Shen J, Chapin A, Boczek NJ, Schimmenti LA, Murry JB, Hasadsri L, Nara K, Kenna M, Booth KT, Azaiez H, Griffith A, Avraham KB, Kremer H, Rehm HL, Amr SS, Abou Tayoun AN; et al.

Hum Mutat. 2018 Nov;39(11):1593-1613. doi: 10.1002/humu.23630.

PubMed [citation]

PMID:: 30311386
PMCID:: PMC6188673

Details of each submission

From Centre for Mendelian Genomics,University Medical Centre Ljubljana, SCV001368348.1

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

Description

This variant was classified as: Uncertain significance. The available evidence on this varinat's pathogenicity is insufficient or conflicting. The following ACMG criteria were applied in classifying this variant: PM1,PP2,PP3. This variant was detected in hemizygous state.

#	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

Last Updated: Dec 7, 2020

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