NM_000410.4(HFE):c.187C>G (p.His63Asp) AND Variegate porphyria

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 13, 2020
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:: RCV002272003.9

Allele description [Variation Report for NM_000410.4(HFE):c.187C>G (p.His63Asp)]

NM_000410.4(HFE):c.187C>G (p.His63Asp)

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.187C>G (p.His63Asp)

HGVS:

NC_000006.12:g.26090951C>G
NG_008720.2:g.8671C>G
NM_000410.4:c.187C>GMANE SELECT
NM_001300749.3:c.187C>G
NM_001384164.1:c.187C>G
NM_001406751.1: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_000401.1:p.His63Asp
NP_000401.1:p.His63Asp
NP_001287678.1:p.His63Asp
NP_001287678.1:p.His63Asp
NP_001371093.1:p.His63Asp
NP_001393680.1: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_000410.3:c.187C>G
NM_001300749.2:c.187C>G
NM_001300749.2:c.187C>G
NM_001384164.1:c.187C>G
NM_139011.2:c.77-2168C>G
NR_144383.1:n.84G>C
Q30201:p.His63Asp
c.187C>G(H63D)

Protein change:

H40D; His63Asp

Links:

Genetic Testing Registry (GTR): GTR000021464; Genetic Testing Registry (GTR): GTR000558915; 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_000410.4:c.187C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001300749.3:c.187C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001384164.1:c.187C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406751.1: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]

Functional consequence:

Unknown function

Condition(s)

Name:: Variegate porphyria (VP)
Synonyms:: Porphyria, South African type; Protoporphyrinogen oxidase deficiency; PPOX deficiency
Identifiers:: MONDO: MONDO:0008297; MedGen: C0162532; Orphanet: 79473; OMIM: 176200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002556586	Genetics and Molecular Pathology, SA Pathology See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 13, 2020)	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

SCV002556586

Genetics and Molecular Pathology, SA Pathology

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 13, 2020)

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Genetics and Molecular Pathology, SA Pathology, SCV002556586.2

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

Description

Contributing pathogenic variant when co-inherited with other pathogenic variants in HFE or PPOX genes, but not pathogenic alone, even in the homozygous 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: Nov 24, 2024

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