NM_003982.4(SLC7A7):c.149T>C (p.Met50Thr) AND Lysinuric protein intolerance

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 28, 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:: RCV000707106.8

Allele description [Variation Report for NM_003982.4(SLC7A7):c.149T>C (p.Met50Thr)]

NM_003982.4(SLC7A7):c.149T>C (p.Met50Thr)

Gene:

SLC7A7:solute carrier family 7 member 7 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q11.2

Genomic location:

Preferred name:

NM_003982.4(SLC7A7):c.149T>C (p.Met50Thr)

HGVS:

NC_000014.9:g.22813250A>G
NG_012851.2:g.21571T>C
NM_001126105.3:c.149T>C
NM_001126106.4:c.149T>C
NM_003982.4:c.149T>CMANE SELECT
NP_001119577.1:p.Met50Thr
NP_001119578.1:p.Met50Thr
NP_001119578.1:p.Met50Thr
NP_003973.3:p.Met50Thr
LRG_695t2:c.149T>C
LRG_695t3:c.149T>C
LRG_695:g.21571T>C
LRG_695p2:p.Met50Thr
LRG_695p3:p.Met50Thr
NC_000014.8:g.23282459A>G
NM_001126106.2:c.149T>C

Protein change:

M50T

Links:

dbSNP: rs386833811

NCBI 1000 Genomes Browser:

rs386833811

Molecular consequence:

NM_001126105.3:c.149T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126106.4:c.149T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003982.4:c.149T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Lysinuric protein intolerance (LPI)
Synonyms:: Dibasicamino aciduria II
Identifiers:: MONDO: MONDO:0009109; MedGen: C0268647; Orphanet: 470; OMIM: 222700

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000836189	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 28, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002091202	Natera, Inc.	no assertion criteria provided	Uncertain significance (Oct 15, 2021)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000836189

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 28, 2021)

germline

clinical testing

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

SCV002091202

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Oct 15, 2021)

germline

clinical testing

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, SCV000836189.3

#	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 methionine with threonine at codon 50 of the SLC7A7 protein (p.Met50Thr). The methionine residue is moderately conserved and there is a moderate physicochemical difference between methionine and threonine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with SLC7A7-related conditions. 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. 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

From Natera, Inc., SCV002091202.1

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

#	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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