NM_003982.4(SLC7A7):c.96G>A (p.Lys32=) AND Lysinuric protein intolerance

Germline classification:: Benign (4 submissions)
Last evaluated:: Jan 30, 2025
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001114967.15

Allele description [Variation Report for NM_003982.4(SLC7A7):c.96G>A (p.Lys32=)]

NM_003982.4(SLC7A7):c.96G>A (p.Lys32=)

Genes:

LOC130055323:ATAC-STARR-seq lymphoblastoid silent region 5589 [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.96G>A (p.Lys32=)

Other names:

p.K32K:AAG>AAA

HGVS:

NC_000014.9:g.22813303C>T
NG_012851.2:g.21518G>A
NM_001126105.3:c.96G>A
NM_001126106.4:c.96G>A
NM_003982.4:c.96G>AMANE SELECT
NP_001119577.1:p.Lys32=
NP_001119577.1:p.Lys32=
NP_001119578.1:p.Lys32=
NP_001119578.1:p.Lys32=
NP_003973.3:p.Lys32=
LRG_695t1:c.96G>A
LRG_695t2:c.96G>A
LRG_695t3:c.96G>A
LRG_695:g.21518G>A
LRG_695p1:p.Lys32=
LRG_695p2:p.Lys32=
LRG_695p3:p.Lys32=
NC_000014.8:g.23282512C>T
NM_001126105.2:c.96G>A
NM_001126106.2:c.96G>A

Links:

dbSNP: rs45479698

NCBI 1000 Genomes Browser:

rs45479698

Molecular consequence:

NM_001126105.3:c.96G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126106.4:c.96G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_003982.4:c.96G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Lysinuric protein intolerance (LPI)
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
SCV001272894	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Jan 13, 2018)	germline	clinical testing	Citation Link,
SCV001459974	Natera, Inc.	no assertion criteria provided	Benign (Sep 16, 2020)	germline	clinical testing
SCV001717799	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 30, 2025)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002045753	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Nov 7, 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
not provided	germline	no	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

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 Illumina Laboratory Services, Illumina, SCV001272894.1

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	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., SCV001459974.1

#	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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001717799.5

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

#	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 Genome-Nilou Lab, SCV002045753.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 29, 2025

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