NC_000014.8:g.(?_92436017)_(92436257_?)del AND Achondrogenesis, type IA

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 20, 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:: RCV004578079.2

Allele description [Variation Report for NC_000014.8:g.(?_92436017)_(92436257_?)del]

NC_000014.8:g.(?_92436017)_(92436257_?)del

Gene:: TRIP11:thyroid hormone receptor interactor 11 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 14q32.12
Genomic location:: Chr14: 92436017 - 92436257 (on Assembly GRCh37)
Preferred name:: NC_000014.8:g.(?_92436017)_(92436257_?)del
HGVS:: NC_000014.8:g.(?_92436017)_(92436257_?)del
This HGVS expression did not pass validation

Condition(s)

Name:: Achondrogenesis, type IA (ACG1A)
Synonyms:: Achondrogenesis type 1A; Achondrogenesis Houston-Harris type
Identifiers:: MONDO: MONDO:0008701; MedGen: C0265273; Orphanet: 932; Orphanet: 93299; OMIM: 200600

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005065547	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (May 20, 2023)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23956106, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005065547

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(May 20, 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

The phenotype range of achondrogenesis 1A.

Grigelioniene G, Geiberger S, Papadogiannakis N, Mäkitie O, Nishimura G, Nordgren A, Conner P.

Am J Med Genet A. 2013 Oct;161A(10):2554-8. doi: 10.1002/ajmg.a.36106. Epub 2013 Aug 16.

PubMed [citation]

PMID:: 23956106

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, SCV005065547.1

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

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 21 of the TRIP11 gene, which includes the termination codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. While this deletion is not anticipated to lead to nonsense mediated decay, it is expected to alter mRNA translation or result in a truncated protein product. A similar copy number variant has been observed in individual(s) with clinical features of achondrogenesis (PMID: 23956106). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#	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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