NM_001122764.3(PPOX):c.502C>T (p.Arg168Cys) AND Variegate porphyria

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Jul 1, 1996
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000009231.9

Allele description [Variation Report for NM_001122764.3(PPOX):c.502C>T (p.Arg168Cys)]

NM_001122764.3(PPOX):c.502C>T (p.Arg168Cys)

Gene:

PPOX:protoporphyrinogen oxidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q23.3

Genomic location:

Preferred name:

NM_001122764.3(PPOX):c.502C>T (p.Arg168Cys)

HGVS:

NC_000001.11:g.161168462C>T
NG_012877.2:g.7072C>T
NM_000309.5:c.502C>T
NM_001122764.3:c.502C>TMANE SELECT
NM_001350128.2:c.403C>T
NM_001350129.2:c.94C>T
NM_001350130.2:c.16C>T
NM_001350131.2:c.16C>T
NM_001365398.1:c.502C>T
NM_001365399.1:c.502C>T
NM_001365400.1:c.94C>T
NM_001365401.1:c.16C>T
NP_000300.1:p.Arg168Cys
NP_001116236.1:p.Arg168Cys
NP_001337057.1:p.Arg135Cys
NP_001337058.1:p.Arg32Cys
NP_001337059.1:p.Arg6Cys
NP_001337060.1:p.Arg6Cys
NP_001352327.1:p.Arg168Cys
NP_001352328.1:p.Arg168Cys
NP_001352329.1:p.Arg32Cys
NP_001352330.1:p.Arg6Cys
LRG_1078t1:c.502C>T
LRG_1078:g.7072C>T
LRG_1078p1:p.Arg168Cys
NC_000001.10:g.161138252C>T
P50336:p.Arg168Cys

Protein change:

R135C; ARG168CYS

Links:

UniProtKB: P50336#VAR_003688; OMIM: 600923.0004; dbSNP: rs121918325

NCBI 1000 Genomes Browser:

rs121918325

Molecular consequence:

NM_000309.5:c.502C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001122764.3:c.502C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001350128.2:c.403C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001350129.2:c.94C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001350130.2:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001350131.2:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001365398.1:c.502C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001365399.1:c.502C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001365400.1:c.94C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001365401.1:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001479915	University of Washington Center for Mendelian Genomics, University of Washington	no assertion criteria provided	Likely pathogenic	inherited	research	PubMed (1) [See all records that cite this PMID]
SCV004030235	OMIM	no assertion criteria provided	Pathogenic (Jul 1, 1996)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 8673113, 8817334

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001479915

University of Washington Center for Mendelian Genomics, University of Washington

no assertion criteria provided

Likely pathogenic

inherited

research

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

SCV004030235

OMIM

no assertion criteria provided

Pathogenic
(Jul 1, 1996)

germline

literature only

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	inherited	yes	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

Sequence variants in nine different genes underlying rare skin disorders in 10 consanguineous families.

Shah K, Mehmood S, Jan A, Abbe I, Hussain Ali R, Khan A, Chishti MS, Lee K, Ahmad F, Ansar M; University of Washington Center for Mendelian Genomics., Shahzad S, Nickerson DA, Bamshad MJ, Coucke PJ, Santos-Cortez RLP, Spritz RA, Leal SM, Ahmad W.

Int J Dermatol. 2017 Dec;56(12):1406-1413. doi: 10.1111/ijd.13778.

PubMed [citation]

PMID:: 29130490
PMCID:: PMC6094939

A R59W mutation in human protoporphyrinogen oxidase results in decreased enzyme activity and is prevalent in South Africans with variegate porphyria.

Meissner PN, Dailey TA, Hift RJ, Ziman M, Corrigall AV, Roberts AG, Meissner DM, Kirsch RE, Dailey HA.

Nat Genet. 1996 May;13(1):95-7.

PubMed [citation]

PMID:: 8673113

See all PubMed Citations (3)

Details of each submission

From University of Washington Center for Mendelian Genomics, University of Washington, SCV001479915.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From OMIM, SCV004030235.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (2)

Description

For discussion of the C-to-T transition in codon 168 of the PPOX gene, resulting in an arg168-to-cys (R168C) substitution, that was found in compound heterozygous state in a girl of Afrikaner origin with childhood-onset variegate porphyria (VPCO; 620483) by Meissner et al. (1996), see 600923.0003.

Warnich et al. (1996) identified heterozygosity for this exon 6 mutation (R168C) in the PPOX gene in 1 of 17 South African patients with variegate porphyria (VP; 176200). This mutation would abolish a DsaI restriction site in genomic DNA of affected individuals, and was shown to be associated with a different haplotype for the exon 1 polymorphism A(26)-C(150) than were the R59W (600923.0003) or H20P (600923.0005) mutations.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 14, 2024

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