NC_000009.11:g.(?_108467858)_(108468054_?)del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 30, 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:: RCV004582128.2

Allele description [Variation Report for NC_000009.11:g.(?_108467858)_(108468054_?)del]

NC_000009.11:g.(?_108467858)_(108468054_?)del

Gene:: TMEM38B:transmembrane protein 38B [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 9q31.2
Genomic location:: Chr9: 108467858 - 108468054 (on Assembly GRCh37)
Preferred name:: NC_000009.11:g.(?_108467858)_(108468054_?)del
HGVS:: NC_000009.11:g.(?_108467858)_(108468054_?)del
This HGVS expression did not pass validation

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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cytochrome oxidase subunit 1, partial (mitochondrion) [Platax orbicularis]
cytochrome oxidase subunit 1, partial (mitochondrion) [Platax orbicularis]
gi|2484104190|gb|WFS29648.1|

Protein
Mus musculus adult male stomach cDNA, RIKEN full-length enriched library, clone:...
Mus musculus adult male stomach cDNA, RIKEN full-length enriched library, clone:2210416O16 product:GASTRICSIN PRECURSOR (EC 3.4.23.3) (PEPSINOGEN C) homolog [Rattus norvegicus], full insert sequence
gi|12843460|dbj|AK008959.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005062729	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 30, 2023)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17611541, 23054245, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005062729

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 30, 2023)

unknown

clinical testing

PubMed (3)
[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

TRIC channels are essential for Ca2+ handling in intracellular stores.

Yazawa M, Ferrante C, Feng J, Mio K, Ogura T, Zhang M, Lin PH, Pan Z, Komazaki S, Kato K, Nishi M, Zhao X, Weisleder N, Sato C, Ma J, Takeshima H.

Nature. 2007 Jul 5;448(7149):78-82.

PubMed [citation]

PMID:: 17611541

Study of autosomal recessive osteogenesis imperfecta in Arabia reveals a novel locus defined by TMEM38B mutation.

Shaheen R, Alazami AM, Alshammari MJ, Faqeih E, Alhashmi N, Mousa N, Alsinani A, Ansari S, Alzahrani F, Al-Owain M, Alzayed ZS, Alkuraya FS.

J Med Genet. 2012 Oct;49(10):630-5. doi: 10.1136/jmedgenet-2012-101142.

PubMed [citation]

PMID:: 23054245

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005062729.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with TMEM38B-related conditions. This variant is a gross deletion of the genomic region encompassing exon(s) 2 of the TMEM38B gene. This deletion is out-of-frame, and is expected to create a premature termination codon and result in an absent or disrupted protein product. Loss-of-function variants in TMEM38B are known to be pathogenic (PMID: 17611541, 23054245).

#	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: Sep 29, 2024

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