NM_001384474.1(LOXHD1):c.1708G>A (p.Asp570Asn) AND not specified

Germline classification:: Benign (1 submission)
Last evaluated:: Dec 21, 2017
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:: RCV000041191.9

Allele description [Variation Report for NM_001384474.1(LOXHD1):c.1708G>A (p.Asp570Asn)]

NM_001384474.1(LOXHD1):c.1708G>A (p.Asp570Asn)

Gene:

LOXHD1:lipoxygenase homology PLAT domains 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

18q21.1

Genomic location:

Preferred name:

NM_001384474.1(LOXHD1):c.1708G>A (p.Asp570Asn)

HGVS:

NC_000018.10:g.46579731C>T
NG_016646.2:g.82303G>A
NM_001384474.1:c.1708G>AMANE SELECT
NM_144612.7:c.1708G>A
NP_001371403.1:p.Asp570Asn
NP_653213.6:p.Asp570Asn
NP_653213.6:p.Asp570Asn
NC_000018.9:g.44159694C>T
NM_144612.6:c.1708G>A
c.1708G>A

Protein change:

D570N

Links:

dbSNP: rs140437150

NCBI 1000 Genomes Browser:

rs140437150

Molecular consequence:

NM_001384474.1:c.1708G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_144612.7:c.1708G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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PHDP Putative homeodomain protein [Drosophila melanogaster]
PHDP Putative homeodomain protein [Drosophila melanogaster]
Gene ID:37788

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000064882	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Dec 21, 2017)	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

SCV000064882

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(Dec 21, 2017)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	4	4	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, SCV000064882.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	PubMed (1)

Description

p.Asp570Asn variant in exon 13 of LOXHD1: This variant is not expected to have c linical significance because it has been identified in 193/16434 (1.2%) African American chromosomes by the genome Aggregation Database (gnomAD, http://gnomad.b roadinstitute.org/; dbSNP rs140437150). ACMG/AMP criteria applied: BA1.

#	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		4	not provided	4	not provided

Last Updated: Sep 29, 2024

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