NC_000011.9:g.(?_85339652)_(86666127_?)del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 15, 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:: RCV003122860.5

Allele description [Variation Report for NC_000011.9:g.(?_85339652)_(86666127_?)del]

NC_000011.9:g.(?_85339652)_(86666127_?)del

Genes:

CREBZF:CREB/ATF bZIP transcription factor [Gene - OMIM - HGNC]
CCDC81:coiled-coil domain containing 81 [Gene - HGNC]
CCDC83:coiled-coil domain containing 83 [Gene - HGNC]
CCDC89:coiled-coil domain containing 89 [Gene - HGNC]
EED:embryonic ectoderm development [Gene - OMIM - HGNC]
FZD4:frizzled class receptor 4 [Gene - OMIM - HGNC]
HIKESHI:heat shock protein nuclear import factor hikeshi [Gene - OMIM - HGNC]
ME3:malic enzyme 3 [Gene - OMIM - HGNC]
PICALM:phosphatidylinositol binding clathrin assembly protein [Gene - OMIM - HGNC]
PRSS23:serine protease 23 [Gene - OMIM - HGNC]
SYTL2:synaptotagmin like 2 [Gene - OMIM - HGNC]
TMEM126A:transmembrane protein 126A [Gene - OMIM - HGNC]
TMEM126B:transmembrane protein 126B [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q14.1-14.2

Genomic location:

Chr11: 85339652 - 86666127 (on Assembly GRCh37)

Preferred name:

NC_000011.9:g.(?_85339652)_(86666127_?)del

HGVS:

NC_000011.9:g.(?_85339652)_(86666127_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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cytochrome b, partial (mitochondrion) [Peromyscus maniculatus blandus]
cytochrome b, partial (mitochondrion) [Peromyscus maniculatus blandus]
gi|89032475|gb|ABD59640.1|

Protein
NADH dehydrogenase subunit 3 (mitochondrion) [Peromyscus maniculatus oreas]
NADH dehydrogenase subunit 3 (mitochondrion) [Peromyscus maniculatus oreas]
gi|1655737|gb|AAB17909.1|

Protein
Solanum habrochaites voucher LA2144 clone 1 phytoene synthase 1 (PSY1) gene, com...
Solanum habrochaites voucher LA2144 clone 1 phytoene synthase 1 (PSY1) gene, complete cds
gi|1905082718|gb|MN782528.1|

Nucleotide
tubulin tyrosine ligase-like family, member 9, isoform CRA_c [Homo sapiens]
tubulin tyrosine ligase-like family, member 9, isoform CRA_c [Homo sapiens]
gi|119596809|gb|EAW76403.1||gnl|WGS |hCP1920771

Protein
cytochrome c oxidase subunit II, partial (mitochondrion) [Peromyscus maniculatus...
cytochrome c oxidase subunit II, partial (mitochondrion) [Peromyscus maniculatus santacruzae]
gi|67633958|gb|AAY78898.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003795720	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 15, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 19327736, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003795720

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 15, 2023)

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

TMEM126A, encoding a mitochondrial protein, is mutated in autosomal-recessive nonsyndromic optic atrophy.

Hanein S, Perrault I, Roche O, Gerber S, Khadom N, Rio M, Boddaert N, Jean-Pierre M, Brahimi N, Serre V, Chretien D, Delphin N, Fares-Taie L, Lachheb S, Rotig A, Meire F, Munnich A, Dufier JL, Kaplan J, Rozet JM.

Am J Hum Genet. 2009 Apr;84(4):493-8. doi: 10.1016/j.ajhg.2009.03.003. Epub 2009 Mar 26.

PubMed [citation]

PMID:: 19327736
PMCID:: PMC2667974

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, SCV003795720.3

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the TMEM126A gene has been identified. Loss-of-function variants in TMEM126A are known to be pathogenic (PMID: 19327736). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with TMEM126A-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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
2	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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