NM_213653.4(HJV):c.1012A>G (p.Ile338Val) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 1, 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:: RCV001298797.5

Allele description

NM_213653.4(HJV):c.1012A>G (p.Ile338Val)

Gene:

HJV:hemojuvelin BMP co-receptor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q21.1

Genomic location:

Preferred name:

NM_213653.4(HJV):c.1012A>G (p.Ile338Val)

HGVS:

NC_000001.11:g.146018346T>C
NG_011568.1:g.8477A>G
NM_001316767.2:c.334A>G
NM_001379352.1:c.1012A>G
NM_145277.5:c.673A>G
NM_202004.4:c.334A>G
NM_213652.4:c.334A>G
NM_213653.4:c.1012A>GMANE SELECT
NP_001303696.1:p.Ile112Val
NP_001366281.1:p.Ile338Val
NP_660320.3:p.Ile225Val
NP_973733.1:p.Ile112Val
NP_998817.1:p.Ile112Val
NP_998818.1:p.Ile338Val
NC_000001.10:g.145416667A>G

Protein change:

I112V

Links:

dbSNP: rs782682125

NCBI 1000 Genomes Browser:

rs782682125

Molecular consequence:

NM_001316767.2:c.334A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001379352.1:c.1012A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_145277.5:c.673A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_202004.4:c.334A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_213652.4:c.334A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_213653.4:c.1012A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

Recent activity

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Homo sapiens family with sequence similarity 219 member A (FAM219A), transcript ...
Homo sapiens family with sequence similarity 219 member A (FAM219A), transcript variant 3, mRNA
gi|1675042635|ref|NM_001184942.2|

Nucleotide
Homo sapiens family with sequence similarity 219 member A (FAM219A), transcript ...
Homo sapiens family with sequence similarity 219 member A (FAM219A), transcript variant 4, mRNA
gi|22218620|ref|NM_147202.1|

Nucleotide
Pseudomonas sp. hata95 16S ribosomal RNA gene, partial sequence
Pseudomonas sp. hata95 16S ribosomal RNA gene, partial sequence
gi|630366534|gb|KJ524266.1|

Nucleotide
Pseudomonas sp. hata94 16S ribosomal RNA gene, partial sequence
Pseudomonas sp. hata94 16S ribosomal RNA gene, partial sequence
gi|630366533|gb|KJ524265.1|

Nucleotide
fbxw4 [Salmo salar]
fbxw4 [Salmo salar]
Gene ID:106576695

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001487864	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 1, 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

SCV001487864

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 1, 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 Invitae, SCV001487864.3

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

Description

This sequence change replaces isoleucine with valine at codon 338 of the HJV protein (p.Ile338Val). The isoleucine residue is highly conserved and there is a small physicochemical difference between isoleucine and valine. This variant is present in population databases (rs782682125, ExAC 0.01%). This variant has not been reported in the literature in individuals affected with HJV-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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 7, 2023

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