NM_005984.5(SLC25A1):c.529del (p.Gly176_Leu177insTer) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 15, 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:: RCV002611331.3

Allele description [Variation Report for NM_005984.5(SLC25A1):c.529del (p.Gly176_Leu177insTer)]

NM_005984.5(SLC25A1):c.529del (p.Gly176_Leu177insTer)

Gene:

SLC25A1:solute carrier family 25 member 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

NM_005984.5(SLC25A1):c.529del (p.Gly176_Leu177insTer)

HGVS:

NC_000022.11:g.19176948del
NG_033863.1:g.6916del
NM_001256534.2:c.550del
NM_001287387.2:c.220del
NM_005984.5:c.529delMANE SELECT
NP_001243463.1:p.Gly183_Leu184insTer
NP_001274316.1:p.Gly73_Leu74insTer
NP_005975.1:p.Gly176_Leu177insTer
NC_000022.10:g.19164461del
NR_033687.2:n.554delC
NR_046298.3:n.453del

Molecular consequence:

NR_046298.3:n.453del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001256534.2:c.550del - nonsense - [Sequence Ontology: SO:0001587]
NM_001287387.2:c.220del - nonsense - [Sequence Ontology: SO:0001587]
NM_005984.5:c.529del - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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PLICBS_005015 [Purpureocillium lilacinum]
PLICBS_005015 [Purpureocillium lilacinum]
Gene ID:28890627

Gene
SBNO1 strawberry notch homolog 1 [Homo sapiens]
SBNO1 strawberry notch homolog 1 [Homo sapiens]
Gene ID:55206

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003504596	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 15, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23561848, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003504596

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 15, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Deficiency in SLC25A1, encoding the mitochondrial citrate carrier, causes combined D-2- and L-2-hydroxyglutaric aciduria.

Nota B, Struys EA, Pop A, Jansen EE, Fernandez Ojeda MR, Kanhai WA, Kranendijk M, van Dooren SJ, Bevova MR, Sistermans EA, Nieuwint AW, Barth M, Ben-Omran T, Hoffmann GF, de Lonlay P, McDonald MT, Meberg A, Muntau AC, Nuoffer JM, Parini R, Read MH, Renneberg A, et al.

Am J Hum Genet. 2013 Apr 4;92(4):627-31. doi: 10.1016/j.ajhg.2013.03.009.

PubMed [citation]

PMID:: 23561848
PMCID:: PMC3617390

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, SCV003504596.2

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

Description

This sequence change creates a premature translational stop signal (p.Leu177*) in the SLC25A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC25A1 are known to be pathogenic (PMID: 23561848). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with SLC25A1-related conditions. This variant is not present in population databases (gnomAD no frequency).

#	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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