NM_006214.4(PHYH):c.717C>G (p.Tyr239Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 3, 2023
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:: RCV003694286.1

Allele description [Variation Report for NM_006214.4(PHYH):c.717C>G (p.Tyr239Ter)]

NM_006214.4(PHYH):c.717C>G (p.Tyr239Ter)

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.717C>G (p.Tyr239Ter)

HGVS:

NC_000010.11:g.13283801G>C
NG_012862.1:g.21330C>G
NM_001037537.2:c.417C>G
NM_001323080.2:c.417C>G
NM_001323082.2:c.723C>G
NM_001323083.2:c.453C>G
NM_001323084.2:c.423C>G
NM_006214.4:c.717C>GMANE SELECT
NP_001032626.1:p.Tyr139Ter
NP_001310009.1:p.Tyr139Ter
NP_001310011.1:p.Tyr241Ter
NP_001310012.1:p.Tyr151Ter
NP_001310013.1:p.Tyr141Ter
NP_006205.1:p.Tyr239Ter
NC_000010.10:g.13325801G>C

Protein change:

Y139*

Molecular consequence:

NM_001037537.2:c.417C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001323080.2:c.417C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001323082.2:c.723C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001323083.2:c.453C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001323084.2:c.423C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_006214.4:c.717C>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004436318	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 3, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9326940, 14974078, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004436318

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 3, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Refsum disease is caused by mutations in the phytanoyl-CoA hydroxylase gene.

Jansen GA, Ofman R, Ferdinandusse S, Ijlst L, Muijsers AO, Skjeldal OH, Stokke O, Jakobs C, Besley GT, Wraith JE, Wanders RJ.

Nat Genet. 1997 Oct;17(2):190-3.

PubMed [citation]

PMID:: 9326940

Molecular basis of Refsum disease: sequence variations in phytanoyl-CoA hydroxylase (PHYH) and the PTS2 receptor (PEX7).

Jansen GA, Waterham HR, Wanders RJ.

Hum Mutat. 2004 Mar;23(3):209-18. Review.

PubMed [citation]

PMID:: 14974078

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004436318.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PHYH-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr239*) in the PHYH gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PHYH are known to be pathogenic (PMID: 9326940, 14974078).

#	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 28, 2024

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