NM_006214.4(PHYH):c.733C>T (p.Arg245Trp) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 18, 2022
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:: RCV002621584.1

Allele description

NM_006214.4(PHYH):c.733C>T (p.Arg245Trp)

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.733C>T (p.Arg245Trp)

HGVS:

NC_000010.11:g.13283785G>A
NG_012862.1:g.21346C>T
NM_001037537.2:c.433C>T
NM_001323080.2:c.433C>T
NM_001323082.2:c.739C>T
NM_001323083.2:c.469C>T
NM_001323084.2:c.439C>T
NM_006214.4:c.733C>TMANE SELECT
NP_001032626.1:p.Arg145Trp
NP_001310009.1:p.Arg145Trp
NP_001310011.1:p.Arg247Trp
NP_001310012.1:p.Arg157Trp
NP_001310013.1:p.Arg147Trp
NP_006205.1:p.Arg245Trp
NC_000010.10:g.13325785G>A

Protein change:

R145W

Molecular consequence:

NM_001037537.2:c.433C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001323080.2:c.433C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001323082.2:c.739C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001323083.2:c.469C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001323084.2:c.439C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006214.4:c.733C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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PREDICTED: Homo sapiens myelin expression factor 2 (MYEF2), transcript variant X...
PREDICTED: Homo sapiens myelin expression factor 2 (MYEF2), transcript variant X9, mRNA
gi|2462544486|ref|XM_054378135.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002950656	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 18, 2022)	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

SCV002950656

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 18, 2022)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002950656.1

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

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 245 of the PHYH protein (p.Arg245Trp). This variant is present in population databases (rs753737115, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with PHYH-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C35"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Feb 13, 2023

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