NM_006214.4(PHYH):c.785T>C (p.Leu262Pro) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 15, 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:: RCV003091752.2

Allele description [Variation Report for NM_006214.4(PHYH):c.785T>C (p.Leu262Pro)]

NM_006214.4(PHYH):c.785T>C (p.Leu262Pro)

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.785T>C (p.Leu262Pro)

HGVS:

NC_000010.11:g.13283733A>G
NG_012862.1:g.21398T>C
NM_001037537.2:c.485T>C
NM_001323080.2:c.485T>C
NM_001323082.2:c.791T>C
NM_001323083.2:c.521T>C
NM_001323084.2:c.491T>C
NM_006214.4:c.785T>CMANE SELECT
NP_001032626.1:p.Leu162Pro
NP_001310009.1:p.Leu162Pro
NP_001310011.1:p.Leu264Pro
NP_001310012.1:p.Leu174Pro
NP_001310013.1:p.Leu164Pro
NP_006205.1:p.Leu262Pro
NC_000010.10:g.13325733A>G

Protein change:

L162P

Molecular consequence:

NM_001037537.2:c.485T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001323080.2:c.485T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001323082.2:c.791T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001323083.2:c.521T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001323084.2:c.491T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006214.4:c.785T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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mitochondrial carnitine/acylcarnitine carrier-like protein [Erigeron canadensis]
mitochondrial carnitine/acylcarnitine carrier-like protein [Erigeron canadensis]
gi|2097467687|ref|XP_043629135.1|

Protein
mitochondrial basic amino acids transporter [Arvicanthis niloticus]
mitochondrial basic amino acids transporter [Arvicanthis niloticus]
gi|1842131692|ref|XP_034343788.1|

Protein
Borrelia nietonii YOR plasmid cp60, complete sequence
Borrelia nietonii YOR plasmid cp60, complete sequence
gi|2225474161|gb|CP073151.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003480819	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 15, 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

SCV003480819

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 15, 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, SCV003480819.2

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 262 of the PHYH protein (p.Leu262Pro). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PHYH-related conditions. 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 20, 2024

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