NC_000007.13:g.(?_140434397)_(141759786_?)del AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 6, 2023
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:: RCV004583511.1

Allele description [Variation Report for NC_000007.13:g.(?_140434397)_(141759786_?)del]

NC_000007.13:g.(?_140434397)_(141759786_?)del

Genes:

BRAF:B-Raf proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
CLEC5A:C-type lectin domain containing 5A [Gene - OMIM - HGNC]
DENND11:DENN domain containing 11 [Gene - OMIM - HGNC]
WEE2:WEE2 oocyte meiosis inhibiting kinase [Gene - OMIM - HGNC]
AGK:acylglycerol kinase [Gene - OMIM - HGNC]
MGAM:maltase-glucoamylase [Gene - OMIM - HGNC]
MRPS33:mitochondrial ribosomal protein S33 [Gene - OMIM - HGNC]
OR9A4:olfactory receptor family 9 subfamily A member 4 [Gene - HGNC]
PRSS37:serine protease 37 [Gene - HGNC]
SSBP1:single stranded DNA binding protein 1 [Gene - OMIM - HGNC]
TAS2R38:taste 2 receptor member 38 [Gene - OMIM - HGNC]
TAS2R3:taste 2 receptor member 3 [Gene - OMIM - HGNC]
TAS2R4:taste 2 receptor member 4 [Gene - OMIM - HGNC]
TAS2R5:taste 2 receptor member 5 [Gene - OMIM - HGNC]
TMEM178B:transmembrane protein 178B [Gene - HGNC]

Variant type:

Deletion

Cytogenetic location:

7q34

Genomic location:

Chr7: 140434397 - 141759786 (on Assembly GRCh37)

Preferred name:

NC_000007.13:g.(?_140434397)_(141759786_?)del

HGVS:

NC_000007.13:g.(?_140434397)_(141759786_?)del

Condition(s)

Name:: Sengers syndrome
Synonyms:: Cardiomyopathy and cataract; MITOCHONDRIAL DNA DEPLETION SYNDROME 10 (CARDIOMYOPATHIC TYPE)
Identifiers:: MONDO: MONDO:0008922; MedGen: C1859317; Orphanet: 1369; OMIM: 212350

Name:: Cataract 38
Synonyms:: Cataract, autosomal recessive congenital 5; Cataract 38, autosomal recessive
Identifiers:: MONDO: MONDO:0013859; MedGen: C3553494; Orphanet: 91492; OMIM: 614691

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005064617	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 6, 2023)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22284826, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005064617

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 6, 2023)

unknown

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Lack of the mitochondrial protein acylglycerol kinase causes Sengers syndrome.

Mayr JA, Haack TB, Graf E, Zimmermann FA, Wieland T, Haberberger B, Superti-Furga A, Kirschner J, Steinmann B, Baumgartner MR, Moroni I, Lamantea E, Zeviani M, Rodenburg RJ, Smeitink J, Strom TM, Meitinger T, Sperl W, Prokisch H.

Am J Hum Genet. 2012 Feb 10;90(2):314-20. doi: 10.1016/j.ajhg.2011.12.005. Epub 2012 Jan 26.

PubMed [citation]

PMID:: 22284826
PMCID:: PMC3276657

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 Invitae, SCV005064617.1

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with AGK-related conditions. A gross deletion of the genomic region encompassing the full coding sequence of the AGK gene has been identified. Loss-of-function variants in AGK are known to be pathogenic (PMID: 22284826). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes.

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

Last Updated: Jul 7, 2024

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