NM_000860.6(HPGD):c.584A>C (p.Glu195Ala) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 12, 2021
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:: RCV002010896.6

Allele description [Variation Report for NM_000860.6(HPGD):c.584A>C (p.Glu195Ala)]

NM_000860.6(HPGD):c.584A>C (p.Glu195Ala)

Gene:

HPGD:15-hydroxyprostaglandin dehydrogenase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q34.1

Genomic location:

Preferred name:

NM_000860.6(HPGD):c.584A>C (p.Glu195Ala)

HGVS:

NC_000004.12:g.174493229T>G
NG_011689.1:g.34413A>C
NM_000860.4:c.584A>C
NM_000860.6:c.584A>CMANE SELECT
NM_001145816.3:c.499-1135A>C
NM_001256301.1:c.221A>C
NM_001256305.2:c.422-1135A>C
NM_001256306.2:c.380A>C
NM_001256307.2:c.221A>C
NP_000851.2:p.Glu195Ala
NP_001243230.1:p.Glu74Ala
NP_001243235.1:p.Glu127Ala
NP_001243236.1:p.Glu74Ala
NC_000004.11:g.175414380T>G

Protein change:

E127A

Links:

dbSNP: rs750778750

NCBI 1000 Genomes Browser:

rs750778750

Molecular consequence:

NM_001145816.3:c.499-1135A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001256305.2:c.422-1135A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000860.6:c.584A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001256301.1:c.221A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001256306.2:c.380A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001256307.2:c.221A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Homo sapiens activating transcription factor 2 (ATF2), transcript variant 6, mRN...
Homo sapiens activating transcription factor 2 (ATF2), transcript variant 6, mRNA
gi|1890265736|ref|NM_001256094.2|

Nucleotide
Homo sapiens mRNA for cell division cycle associated protein 7 isoform 2 variant...
Homo sapiens mRNA for cell division cycle associated protein 7 isoform 2 variant, clone: FCC123E09
gi|62898779|dbj|AK223524.1|

Nucleotide
citrate transporter family protein [Klebsiella pneumoniae]
citrate transporter family protein [Klebsiella pneumoniae]
gi|1430039923|emb|SSF17606.1||gnl|W BK|SSF17606

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002289398	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 12, 2021)	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

SCV002289398

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 12, 2021)

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, SCV002289398.3

#	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 tolerated. This sequence change replaces glutamic acid with alanine at codon 195 of the HPGD protein (p.Glu195Ala). The glutamic acid residue is highly conserved and there is a moderate physicochemical difference between glutamic acid and alanine. This variant is present in population databases (rs750778750, ExAC 0.02%). This variant has not been reported in the literature in individuals affected with HPGD-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: Sep 29, 2024

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