NM_000088.4(COL1A1):c.2089C>T (p.Arg697Ter) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Aug 28, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000497565.8

Allele description [Variation Report for NM_000088.4(COL1A1):c.2089C>T (p.Arg697Ter)]

NM_000088.4(COL1A1):c.2089C>T (p.Arg697Ter)

Gene:

COL1A1:collagen type I alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.33

Genomic location:

Preferred name:

NM_000088.4(COL1A1):c.2089C>T (p.Arg697Ter)

HGVS:

NC_000017.11:g.50191826G>A
NG_007400.1:g.14814C>T
NM_000088.4:c.2089C>TMANE SELECT
NP_000079.2:p.Arg697Ter
NP_000079.2:p.Arg697Ter
LRG_1t1:c.2089C>T
LRG_1:g.14814C>T
LRG_1p1:p.Arg697Ter
NC_000017.10:g.48269187G>A
NM_000088.3:c.2089C>T

Protein change:

R697*

Links:

dbSNP: rs72651642

NCBI 1000 Genomes Browser:

rs72651642

Molecular consequence:

NM_000088.4:c.2089C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Same Parent, Connectivity for PubChem Compound (Select 171068065) (2)
PubChem Compound
phosphatidylinositol 3-kinase regulatory subunit alpha isoform 1 [Homo sapiens]
phosphatidylinositol 3-kinase regulatory subunit alpha isoform 1 [Homo sapiens]
gi|32455248|ref|NP_852664.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000341062	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Apr 1, 2016)	germline	clinical testing	Citation Link,
SCV000589583	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Aug 28, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000341062

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Apr 1, 2016)

germline

clinical testing

Citation Link,

SCV000589583

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Aug 28, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000341062.4

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

#	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		2	not provided	not provided	not provided

From GeneDx, SCV000589583.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28378289, 33939306, 27510842, 8808594, 21667357, 25944380, 30715774, 37270749, 35909573, 9443882, 28810924, 32166892, 37334733, 36951356)

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

Last Updated: Oct 20, 2024

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