NM_006214.4(PHYH):c.760G>A (p.Asp254Asn) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 25, 2024
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:: RCV001212402.6

Allele description [Variation Report for NM_006214.4(PHYH):c.760G>A (p.Asp254Asn)]

NM_006214.4(PHYH):c.760G>A (p.Asp254Asn)

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.760G>A (p.Asp254Asn)

HGVS:

NC_000010.11:g.13283758C>T
NG_012862.1:g.21373G>A
NM_001037537.2:c.460G>A
NM_001323080.2:c.460G>A
NM_001323082.2:c.766G>A
NM_001323083.2:c.496G>A
NM_001323084.2:c.466G>A
NM_006214.4:c.760G>AMANE SELECT
NP_001032626.1:p.Asp154Asn
NP_001310009.1:p.Asp154Asn
NP_001310011.1:p.Asp256Asn
NP_001310012.1:p.Asp166Asn
NP_001310013.1:p.Asp156Asn
NP_006205.1:p.Asp254Asn
NC_000010.10:g.13325758C>T
NM_006214.3:c.760G>A

Protein change:

D154N

Links:

dbSNP: rs139329047

NCBI 1000 Genomes Browser:

rs139329047

Molecular consequence:

NM_001037537.2:c.460G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323080.2:c.460G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323082.2:c.766G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323083.2:c.496G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323084.2:c.466G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006214.4:c.760G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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S41 family peptidase [Exiguobacterium marinum]
S41 family peptidase [Exiguobacterium marinum]
gi|2446541101|gnl|PRJNA933108|PTI97 5|gb|WDH75159.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001383985	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 25, 2024)	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

SCV001383985

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 25, 2024)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001383985.5

#	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 aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 254 of the PHYH protein (p.Asp254Asn). This variant is present in population databases (rs139329047, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with PHYH-related conditions. ClinVar contains an entry for this variant (Variation ID: 942416). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PHYH protein function with a positive predictive value of 80%. 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: Sep 29, 2024

ClinVar

Relating variation to medicine