NM_005888.4(SLC25A3):c.279G>T (p.Met93Ile) AND not specified

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Oct 14, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000195983.3

Allele description [Variation Report for NM_005888.4(SLC25A3):c.279G>T (p.Met93Ile)]

NM_005888.4(SLC25A3):c.279G>T (p.Met93Ile)

Genes:

LOC130008523:ATAC-STARR-seq lymphoblastoid active region 6847 [Gene]
SLC25A3:solute carrier family 25 member 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q23.1

Genomic location:

Preferred name:

NM_005888.4(SLC25A3):c.279G>T (p.Met93Ile)

Other names:

p.M93I:ATG>ATT

HGVS:

NC_000012.12:g.98595554G>T
NG_011702.1:g.6930G>T
NM_002635.4:c.158-173G>TMANE SELECT
NM_005888.4:c.279G>T
NM_213611.3:c.158-173G>T
NP_005879.1:p.Met93Ile
NP_005879.1:p.Met93Ile
NC_000012.11:g.98989332G>T
NM_005888.3:c.279G>T

Protein change:

M93I

Links:

dbSNP: rs750003586

NCBI 1000 Genomes Browser:

rs750003586

Molecular consequence:

NM_002635.4:c.158-173G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_213611.3:c.158-173G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_005888.4:c.279G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000252273	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely benign (Jul 28, 2014)	germline	clinical testing	Citation Link,
SCV004951642	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Oct 14, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000252273

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely benign
(Jul 28, 2014)

germline

clinical testing

Citation Link,

SCV004951642

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Oct 14, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000252273.11

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Ambry Genetics, SCV004951642.1

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

Description

The c.279G>T (p.M93I) alteration is located in exon 3 (coding exon 2) of the SLC25A3 gene. This alteration results from a G to T substitution at nucleotide position 279, causing the methionine (M) at amino acid position 93 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

#	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: May 7, 2024

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