NM_006214.4(PHYH):c.703G>A (p.Gly235Arg) AND Phytanic acid storage disease

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 6, 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:: RCV000778275.4

Allele description [Variation Report for NM_006214.4(PHYH):c.703G>A (p.Gly235Arg)]

NM_006214.4(PHYH):c.703G>A (p.Gly235Arg)

Gene:

PHYH:phytanoyl-CoA 2-hydroxylase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10p13

Genomic location:

Preferred name:

NM_006214.4(PHYH):c.703G>A (p.Gly235Arg)

HGVS:

NC_000010.11:g.13283815C>T
NG_012862.1:g.21316G>A
NM_001037537.2:c.403G>A
NM_001323080.2:c.403G>A
NM_001323082.2:c.709G>A
NM_001323083.2:c.439G>A
NM_001323084.2:c.409G>A
NM_006214.4:c.703G>AMANE SELECT
NP_001032626.1:p.Gly135Arg
NP_001310009.1:p.Gly135Arg
NP_001310011.1:p.Gly237Arg
NP_001310012.1:p.Gly147Arg
NP_001310013.1:p.Gly137Arg
NP_006205.1:p.Gly235Arg
NC_000010.10:g.13325815C>T
NM_006214.3:c.703G>A

Protein change:

G135R

Links:

dbSNP: rs750819521

NCBI 1000 Genomes Browser:

rs750819521

Molecular consequence:

NM_001037537.2:c.403G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323080.2:c.403G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323082.2:c.709G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323083.2:c.439G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323084.2:c.409G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006214.4:c.703G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Phytanic acid storage disease
Synonyms:: HMSN IV; REFSUM DISEASE, CLASSIC; Disorder of cornification 11 (phytanic acid type); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009958; MedGen: C0034960; Orphanet: 773; OMIM: 266500

Recent activity

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NADH dehydrogenase (chloroplast) [Antiphiona fragrans]
NADH dehydrogenase (chloroplast) [Antiphiona fragrans]
gi|948545600|emb|CEF89989.1|

Protein
Calvitimela armeniaca voucher O L-204644b elongation factor 1 alpha (tef-1) gene...
Calvitimela armeniaca voucher O L-204644b elongation factor 1 alpha (tef-1) gene, partial cds
gi|2609769598|gb|OR738423.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000914449	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 09 May 2019)	Uncertain significance (Nov 6, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000914449

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)

Uncertain significance
(Nov 6, 2018)

germline

clinical testing

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

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Next-generation sequencing-based molecular diagnosis of 82 retinitis pigmentosa probands from Northern Ireland.

Zhao L, Wang F, Wang H, Li Y, Alexander S, Wang K, Willoughby CE, Zaneveld JE, Jiang L, Soens ZT, Earle P, Simpson D, Silvestri G, Chen R.

Hum Genet. 2015 Feb;134(2):217-30. doi: 10.1007/s00439-014-1512-7. Epub 2014 Dec 4.

PubMed [citation]

PMID:: 25472526
PMCID:: PMC4347882

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000914449.1

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

Description

The PHYH c.703G>A (p.Gly235Arg) missense variant has been reported in one study, (referred to as p.Gly135Arg in this study), in which it is found in a homozygous state in one individual initially diagnosed with retinitis pigmentosa (Zhao et al. 2014). However, when the p.Gly235Arg variant was identified, the individual's phenotype was revisited and he was noted to have mild cerebellar ataxia and hearing loss later in life leading to a subsequent diagnosis of Refsum disease. Control data are not available for this variant which is reported at a frequency of 0.00003 in the European (non-Finnish) population from the Exome Aggregation Consortium, but this is based on two alleles only in an area of good sequence coverage so the variant is presumed to be rare. The evidence for this variant is limited. The p.Gly235Arg variant is classified as a variant of unknown significance but suspicious for pathogenicity for Refsum disease. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

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

Last Updated: Sep 29, 2024

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