NM_003705.5(SLC25A12):c.1935_2030del (p.Phe646_Thr677del) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 22, 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:: RCV002038082.6

Allele description [Variation Report for NM_003705.5(SLC25A12):c.1935_2030del (p.Phe646_Thr677del)]

NM_003705.5(SLC25A12):c.1935_2030del (p.Phe646_Thr677del)

Gene:

SLC25A12:solute carrier family 25 member 12 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2q31.1

Genomic location:

Preferred name:

NM_003705.5(SLC25A12):c.1935_2030del (p.Phe646_Thr677del)

HGVS:

NC_000002.12:g.171785288_171785383del
NG_011781.2:g.113928_114023del
NM_003705.5:c.1935_2030delMANE SELECT
NP_003696.2:p.Phe646_Thr677del
NC_000002.11:g.172641791_172641886del
NC_000002.11:g.172641798_172641893del
NR_047549.2:n.1849_1944del

Links:

dbSNP: rs2105829329

NCBI 1000 Genomes Browser:

rs2105829329

Molecular consequence:

NM_003705.5:c.1935_2030del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_047549.2:n.1849_1944del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Danio rerio testis expressed 2 (tex2), transcript variant X4, mRNA
PREDICTED: Danio rerio testis expressed 2 (tex2), transcript variant X4, mRNA
gi|2800577693|ref|XM_005164255.5|

Nucleotide
Bacillus oceanisediminis strain V3 16S ribosomal RNA gene, partial sequence
Bacillus oceanisediminis strain V3 16S ribosomal RNA gene, partial sequence
gi|766546119|gb|KP120947.1|

Nucleotide
Bacillus licheniformis strain Z7B-15 16S ribosomal RNA gene, partial sequence
Bacillus licheniformis strain Z7B-15 16S ribosomal RNA gene, partial sequence
gi|326582777|gb|HQ238935.1|

Nucleotide
Bacillus licheniformis strain H7B-40 16S ribosomal RNA gene, partial sequence
Bacillus licheniformis strain H7B-40 16S ribosomal RNA gene, partial sequence
gi|326582772|gb|HQ238930.1|

Nucleotide
Myrtoideae ndhF-rpl32 intergenic spacer region, partial sequence; chloroplast.
Myrtoideae ndhF-rpl32 intergenic spacer region, partial sequence; chloroplast.
PopSet: 1867194337

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002272030	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 22, 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

SCV002272030

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 22, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002272030.3

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

Description

This variant is not present in population databases (ExAC no frequency). This variant, c.1935_2030del, results in the deletion of 32 amino acid(s) of the SLC25A12 protein (p.Phe646_Thr677del), but otherwise preserves the integrity of the reading frame. This variant has not been reported in the literature in individuals with SLC25A12-related conditions. 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown.

#	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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