NM_006214.4(PHYH):c.1010_1012dup (p.Leu338_Ter339insHis) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(2) (Last evaluated: Nov 14, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000513200.7

Allele description [Variation Report for NM_006214.4(PHYH):c.1010_1012dup (p.Leu338_Ter339insHis)]

NM_006214.4(PHYH):c.1010_1012dup (p.Leu338_Ter339insHis)

Gene:
PHYH:phytanoyl-CoA 2-hydroxylase [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
10p13
Genomic location:
Preferred name:
NM_006214.4(PHYH):c.1010_1012dup (p.Leu338_Ter339insHis)
HGVS:
  • NC_000010.11:g.13278306_13278308dup
  • NG_012862.1:g.26823_26825dup
  • NM_001037537.1:c.710_712dup
  • NM_001323080.1:c.710_712dup
  • NM_001323082.1:c.1016_1018dup
  • NM_001323083.1:c.746_748dup
  • NM_001323084.1:c.716_718dup
  • NM_006214.4:c.1010_1012dupMANE SELECT
  • NP_001032626.1:p.Leu238_Ter239insHis
  • NP_001310009.1:p.Leu238_Ter239insHis
  • NP_001310011.1:p.Leu340_Ter341insHis
  • NP_001310012.1:p.Leu250_Ter251insHis
  • NP_001310013.1:p.Leu240_Ter241insHis
  • NP_006205.1:p.Leu338_Ter339insHis
  • NC_000010.10:g.13320305_13320306insGAT
  • NC_000010.10:g.13320306_13320308dup
  • NM_006214.3:c.1010_1012dup
  • NM_006214.3:c.1010_1012dupATC
  • p.Asn337_Leu338insHis
Links:
dbSNP: rs566116760
NCBI 1000 Genomes Browser:
rs566116760
Molecular consequence:
  • NM_001037537.1:c.710_712dup - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001323080.1:c.710_712dup - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001323082.1:c.1016_1018dup - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001323083.1:c.746_748dup - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001323084.1:c.716_718dup - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_006214.4:c.1010_1012dup - inframe_insertion - [Sequence Ontology: SO:0001821]
Observations:
5

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000608536CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Uncertain significance
(May 1, 2017)
germlineclinical testing

Citation Link,

SCV001110661Invitaecriteria provided, single submitter
Likely benign
(Nov 14, 2020)
germlineclinical testing

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

SCV001713529Mayo Clinic Laboratories, Mayo Cliniccriteria provided, single submitter
Uncertain significance
(Sep 8, 2020)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown2not providednot providednot providednot providedclinical testing
not providedgermlineyes3not providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

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 CeGaT Praxis fuer Humangenetik Tuebingen, SCV000608536.11

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided3not providednot providednot provided

From Invitae, SCV001110661.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV001713529.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided2not providednot providednot provided

Last Updated: Oct 16, 2021

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