NM_006214.4(PHYH):c.321G>A (p.Ser107=) AND Phytanic acid storage disease

Clinical significance:Benign/Likely benign (Last evaluated: Jan 13, 2018)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000295418.3

Allele description [Variation Report for NM_006214.4(PHYH):c.321G>A (p.Ser107=)]

NM_006214.4(PHYH):c.321G>A (p.Ser107=)

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.321G>A (p.Ser107=)
HGVS:
  • NC_000010.11:g.13294521C>T
  • NG_012862.1:g.10610G>A
  • NM_001037537.1:c.21G>A
  • NM_001037537.2:c.21G>A
  • NM_001323080.2:c.21G>A
  • NM_001323082.2:c.321G>A
  • NM_001323083.2:c.321G>A
  • NM_001323084.2:c.21G>A
  • NM_006214.4:c.321G>AMANE SELECT
  • NP_001032626.1:p.Ser7=
  • NP_001032626.1:p.Ser7=
  • NP_001310009.1:p.Ser7=
  • NP_001310011.1:p.Ser107=
  • NP_001310012.1:p.Ser107=
  • NP_001310013.1:p.Ser7=
  • NP_006205.1:p.Ser107=
  • NC_000010.10:g.13336521C>T
  • NC_000010.10:g.13336521C>T
  • NM_006214.3:c.321G>A
Links:
dbSNP: rs115198308
NCBI 1000 Genomes Browser:
rs115198308
Molecular consequence:
  • NM_001037537.1:c.21G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001037537.2:c.21G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001323080.2:c.21G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001323082.2:c.321G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001323083.2:c.321G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001323084.2:c.21G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_006214.4:c.321G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Phytanic acid storage disease (RDPA)
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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000361488Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Benign
(Jan 13, 2018)
germlineclinical testing

Citation Link,

SCV000745261Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensuscriteria provided, single submitter
Likely benign
(Jun 28, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV000361488.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000745261.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 24, 2021

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