NM_014585.6(SLC40A1):c.139T>C (p.Ser47Pro) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 11, 2019
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:: RCV001027529.1

Allele description [Variation Report for NM_014585.6(SLC40A1):c.139T>C (p.Ser47Pro)]

NM_014585.6(SLC40A1):c.139T>C (p.Ser47Pro)

Gene:

SLC40A1:solute carrier family 40 member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q32.2

Genomic location:

Preferred name:

NM_014585.6(SLC40A1):c.139T>C (p.Ser47Pro)

HGVS:

NC_000002.12:g.189575293A>G
NG_009027.1:g.10519T>C
NM_014585.6:c.139T>CMANE SELECT
NP_055400.1:p.Ser47Pro
LRG_837t1:c.139T>C
LRG_837:g.10519T>C
NC_000002.11:g.190440019A>G
NM_014585.5:c.139T>C

Protein change:

S47P

Links:

dbSNP: rs1574245587

NCBI 1000 Genomes Browser:

rs1574245587

Molecular consequence:

NM_014585.6:c.139T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001190102	MVZ Dr. Eberhard & Partner Dortmund	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 11, 2019)	unknown	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

SCV001190102

MVZ Dr. Eberhard & Partner Dortmund

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 11, 2019)

unknown

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From MVZ Dr. Eberhard & Partner Dortmund, SCV001190102.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing (GTR000327524.2)	PubMed (1)

Description

This variant is absent from controls like ESP, 1000 genomes or gnomAD. In silico analyses are conflicting for c.139T>C (p.(Ser47Pro)) (SIFT: predict tolerated; Mutation Taster: disease causing; Polyphen: HumDiv + HumVar: Probably damaging). In silico analyses give no hint that this variant affects splicing.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	1	not provided	not provided	(GTR000327524.2)	1	not provided	not provided	not provided

Last Updated: Apr 23, 2022

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