NM_000392.5(ABCC2):c.3538C>T (p.Gln1180Ter) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Jan 3, 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:: RCV000728865.7

Allele description [Variation Report for NM_000392.5(ABCC2):c.3538C>T (p.Gln1180Ter)]

NM_000392.5(ABCC2):c.3538C>T (p.Gln1180Ter)

Gene:

ABCC2:ATP binding cassette subfamily C member 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q24.2

Genomic location:

Preferred name:

NM_000392.5(ABCC2):c.3538C>T (p.Gln1180Ter)

HGVS:

NC_000010.11:g.99836214C>T
NG_011798.2:g.58617C>T
NM_000392.4:c.3538C>T
NM_000392.5:c.3538C>TMANE SELECT
NP_000383.2:p.Gln1180Ter
LRG_1208t1:c.3538C>T
LRG_1208:g.58617C>T
LRG_1208p1:p.Gln1180Ter
NC_000010.10:g.101595971C>T
NG_011798.1:g.58509C>T

Protein change:

Q1180*

Links:

dbSNP: rs183923599

NCBI 1000 Genomes Browser:

rs183923599

Molecular consequence:

NM_000392.5:c.3538C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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ST6GALNAC4 [Rhinolophus ferrumequinum]
ST6GALNAC4 [Rhinolophus ferrumequinum]
Gene ID:117032330

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000856483	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Aug 18, 2017)	germline	clinical testing	Citation Link,
SCV003805835	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Feb 24, 2022)	germline	clinical testing	Citation Link,
SCV004650412	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 3, 2024)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 9185779, 16549534, 16952291, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000856483

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Aug 18, 2017)

germline

clinical testing

Citation Link,

SCV003805835

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Feb 24, 2022)

germline

clinical testing

Citation Link,

SCV004650412

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 3, 2024)

germline

clinical testing

PubMed (4)
[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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A mutation in the human canalicular multispecific organic anion transporter gene causes the Dubin-Johnson syndrome.

Paulusma CC, Kool M, Bosma PJ, Scheffer GL, ter Borg F, Scheper RJ, Tytgat GN, Borst P, Baas F, Oude Elferink RP.

Hepatology. 1997 Jun;25(6):1539-42.

PubMed [citation]

PMID:: 9185779

Neonatal Dubin-Johnson syndrome: long-term follow-up and MRP2 mutations study.

Lee JH, Chen HL, Chen HL, Ni YH, Hsu HY, Chang MH.

Pediatr Res. 2006 Apr;59(4 Pt 1):584-9.

PubMed [citation]

PMID:: 16549534

See all PubMed Citations (4)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000856483.1

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

From GeneDx, SCV003805835.1

#	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; Has not been previously published as pathogenic or benign to our knowledge

#	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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004650412.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Gln1180*) in the ABCC2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ABCC2 are known to be pathogenic (PMID: 9185779, 16549534, 16952291). This variant is present in population databases (rs183923599, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with ABCC2-related conditions. ClinVar contains an entry for this variant (Variation ID: 593738). 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

Last Updated: Sep 29, 2024

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