NM_006214.4(PHYH):c.766_767del (p.Val256fs) AND Phytanic acid storage disease

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 12, 2014
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:: RCV000190614.5

Allele description [Variation Report for NM_006214.4(PHYH):c.766_767del (p.Val256fs)]

NM_006214.4(PHYH):c.766_767del (p.Val256fs)

Gene:

PHYH:phytanoyl-CoA 2-hydroxylase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10p13

Genomic location:

Preferred name:

NM_006214.4(PHYH):c.766_767del (p.Val256fs)

HGVS:

NC_000010.11:g.13283752_13283753del
NG_012862.1:g.21379_21380del
NM_001037537.2:c.466_467del
NM_001323080.2:c.466_467del
NM_001323082.2:c.772_773del
NM_001323083.2:c.502_503del
NM_001323084.2:c.472_473del
NM_006214.4:c.766_767delMANE SELECT
NP_001032626.1:p.Val156fs
NP_001310009.1:p.Val156fs
NP_001310011.1:p.Val258fs
NP_001310012.1:p.Val168fs
NP_001310013.1:p.Val158fs
NP_006205.1:p.Val256fs
NC_000010.10:g.13325751_13325752delAC
NC_000010.10:g.13325752_13325753del
NM_006214.3:c.766_767delGT

Protein change:

V156fs

Links:

dbSNP: rs797045100

NCBI 1000 Genomes Browser:

rs797045100

Molecular consequence:

NM_001037537.2:c.466_467del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001323080.2:c.466_467del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001323082.2:c.772_773del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001323083.2:c.502_503del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001323084.2:c.472_473del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_006214.4:c.766_767del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Phytanic acid storage disease
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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000245649	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine - CSER-MedSeq	criteria provided, single submitter (LMM Criteria)	Likely pathogenic (Jun 12, 2014)	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

SCV000245649

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine - CSER-MedSeq

criteria provided, single submitter

(LMM Criteria)

Likely pathogenic
(Jun 12, 2014)

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	not provided	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine - CSER-MedSeq, SCV000245649.1

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

Description

The Val256PhefsX14 variant in PHYH has not been previously identified in the literature or in large population studies. This frameshift variant is predicted to alter the protein’s amino acid sequence beginning at position 256 and lead to a premature termination codon 14 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Complete loss of PHYH function is a known disease mechanism in Refsum disease. In summary, although additional studies are required to fully establish its clinical significance, the Val256PhefsX14 variant is likely pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		1	not provided	1	not provided

Last Updated: Jun 23, 2024

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