16-16163078-G-A

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong

The NM_001171.6(ABCC6):​c.3421C>T​(p.Arg1141*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00161 in 1,613,922 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 5 hom. )

Consequence

ABCC6
NM_001171.6 stop_gained

Scores

2
4
1

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:31

Conservation

PhyloP100: 3.00
Variant links:
Genes affected
ABCC6 (HGNC:57): (ATP binding cassette subfamily C member 6) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). The encoded protein, a member of the MRP subfamily, is involved in multi-drug resistance. Mutations in this gene cause pseudoxanthoma elasticum. Alternatively spliced transcript variants that encode different proteins have been described for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 16 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PP5
Variant 16-16163078-G-A is Pathogenic according to our data. Variant chr16-16163078-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 6559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-16163078-G-A is described in Lovd as [Pathogenic]. Variant chr16-16163078-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ABCC6NM_001171.6 linkc.3421C>T p.Arg1141* stop_gained Exon 24 of 31 ENST00000205557.12 NP_001162.5
ABCC6NM_001351800.1 linkc.3079C>T p.Arg1027* stop_gained Exon 24 of 31 NP_001338729.1
ABCC6NR_147784.1 linkn.3169-1514C>T intron_variant Intron 22 of 28

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ABCC6ENST00000205557.12 linkc.3421C>T p.Arg1141* stop_gained Exon 24 of 31 1 NM_001171.6 ENSP00000205557.7 O95255-1
ABCC6ENST00000622290.5 linkn.3421C>T non_coding_transcript_exon_variant Exon 24 of 32 5 ENSP00000483331.2 A0A8C8Q0G8
ABCC6ENST00000456970.6 linkn.*516-1514C>T intron_variant Intron 22 of 28 2 ENSP00000405002.2 O95255-3

Frequencies

GnomAD3 genomes
AF:
0.00113
AC:
172
AN:
152204
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000981
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00170
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00187
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.00141
AC:
355
AN:
251296
Hom.:
0
AF XY:
0.00154
AC XY:
209
AN XY:
135858
show subpopulations
Gnomad AFR exome
AF:
0.000246
Gnomad AMR exome
AF:
0.000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.00296
Gnomad NFE exome
AF:
0.00232
Gnomad OTH exome
AF:
0.00147
GnomAD4 exome
AF:
0.00166
AC:
2431
AN:
1461600
Hom.:
5
Cov.:
33
AF XY:
0.00171
AC XY:
1245
AN XY:
727076
show subpopulations
Gnomad4 AFR exome
AF:
0.000299
Gnomad4 AMR exome
AF:
0.000246
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000927
Gnomad4 FIN exome
AF:
0.00282
Gnomad4 NFE exome
AF:
0.00195
Gnomad4 OTH exome
AF:
0.00136
GnomAD4 genome
AF:
0.00113
AC:
172
AN:
152322
Hom.:
0
Cov.:
32
AF XY:
0.00107
AC XY:
80
AN XY:
74490
show subpopulations
Gnomad4 AFR
AF:
0.000241
Gnomad4 AMR
AF:
0.000980
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00170
Gnomad4 NFE
AF:
0.00187
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.00195
Hom.:
1
Bravo
AF:
0.00108
TwinsUK
AF:
0.00270
AC:
10
ALSPAC
AF:
0.00208
AC:
8
ESP6500AA
AF:
0.000910
AC:
4
ESP6500EA
AF:
0.00279
AC:
24
ExAC
AF:
0.00139
AC:
169
EpiCase
AF:
0.00191
EpiControl
AF:
0.00190

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:31
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Pathogenic:13
Dec 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

ABCC6: PM3:Very Strong, PVS1, PP1:Strong, PM2:Supporting, PS3:Supporting -

Mar 02, 2016
Eurofins Ntd Llc (ga)
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Mar 06, 2017
Blueprint Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Feb 16, 2023
Clinical Genetics Laboratory, Skane University Hospital Lund
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

-
Genome Diagnostics Laboratory, University Medical Center Utrecht
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Jan 12, 2024
Revvity Omics, Revvity
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Mar 28, 2022
GeneDx
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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; Expression studies of the R1141X variant in leukocytes and cultured fibroblasts from affected individuals homozygous for R1141X demonstrate mRNA instability and absence of the protein in immunohistochemistry studies (Hu et al., 2003); Early speculation that heterozygosity for R1141X may increase the risk of coronary artery disease has not been confirmed in a large cohort study (Trip et al., 2002; Hornstrup et al., 2011).; This variant is associated with the following publications: (PMID: 29800625, 29709427, 31646622, 32646269, 22209248, 12176944, 19929409, 10835643, 25525159, 24352041, 12714611, 23746223, 27133371, 10811882, 23675997, 16086317, 21831958, 26982014, 16854481, 16384891, 16133423, 14631379, 24008425, 28102862, 18800149, 12384774, 30206659, 29722917, 30985656, 31980526, 34440381, 33812167, 34426522, 31589614, 33726816) -

-
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

-
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Feb 02, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Arg1141*) in the ABCC6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ABCC6 are known to be pathogenic (PMID: 11536079, 17617515). This variant is present in population databases (rs72653706, gnomAD 0.3%), and has an allele count higher than expected for a pathogenic variant. This premature translational stop signal has been observed in individual(s) with pseudoxanthoma elasticum (PMID: 10835642, 12714611, 17617515, 22209248, 26982014). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 6559). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -

-
Clinical Genetics, Academic Medical Center
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Autosomal recessive inherited pseudoxanthoma elasticum Pathogenic:10
Jun 23, 2019
Sharon lab, Hadassah-Hebrew University Medical Center
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

Apr 25, 2020
Baylor Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -

Aug 17, 2016
Genetic Services Laboratory, University of Chicago
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jun 24, 2022
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with generalized infantile arterial calcification 2 (MIM#614473), pseudoxanthoma elasticum (MIM#264800) and forme fruste pseudoxanthoma elasticum (MIM#177850). (I) 0106 - This gene is associated with autosomal recessive disease. OIder publications suggest dominant disease (OMIM). (I) 0115 - Variants in this gene are known to have variable expressivity. Intrafamilial variability with age-dependent severity has been well reported (PMID: 28102862). (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (396 heterozygotes, 0 homozygotes). (SP) 0701 - Other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. Many of these variants have been reported times as pathogenic, and are reported in many individuals with pseudoxanthoma elasticum or generalized arterial calcification (Decipher). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported many times as pathogenic, in both homozygous or compound heterozygous individuals with pseudoxanthoma elasticum or generalized arterial calcification of infancy. It represents one of the most common variants within Caucasian populations (ClinVar, PMID: 28102862). (SP) 1102 - Strong phenotype match for this individual. (SP) 1205 - This variant has been shown to be maternally inherited (by segregation analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Jan 13, 2012
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

-
PXE International
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

Aug 04, 2023
Breakthrough Genomics, Breakthrough Genomics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is predicted to cause a premature termination of the protein and the resultant protein will probably lack part of the ABC transmembrane type-1 domain and the entire ABC transporter 2 domain of the protein [UniProt]; this will likely result in loss-of-function. Due to the introduction of a premature stop codon, this aberrant transcript will likely be targeted by the nonsense-mediated mRNA decay (NMD) mechanism [PMID: 15040442]. The identified variant was previously reported in individuals with pseudoxanthoma elasticum and observed to segregate with disease in related individuals [PMID: 10835642, 12714611, 17617515, 22209248, 26982014]. Loss-of-function variants in ABCC6 are known to be pathogenic [PMID: 11536079, 17617515]. -

Sep 04, 2024
Institute of Human Genetics, University of Leipzig Medical Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Criteria applied: PVS1,PM3_STR,PP4; Identified as compund heterozygous with NM_001171.6:c.3413G>A -

Mar 09, 2022
MGZ Medical Genetics Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Mar 08, 2024
Institute of Human Genetics, Heidelberg University
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Arterial calcification, generalized, of infancy, 2 Pathogenic:3
Jan 13, 2012
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Jan 01, 2016
Centre for Mendelian Genomics, University Medical Centre Ljubljana
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant was classified as: Pathogenic. This variant was detected in homozygous state. -

Jun 30, 2023
Baylor Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

ABCC6-related disorder Pathogenic:2
Sep 09, 2024
PreventionGenetics, part of Exact Sciences
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

The ABCC6 c.3421C>T variant is predicted to result in premature protein termination (p.Arg1141*). This variant has been reported to be causative for autosomal recessive pseudoxanthoma elasticum (PXE) (Ringpfeil et al. 2000. PubMed ID: 10811882, ABCC6 gene was reported as MRP6 gene; Hu et al. 2003. PubMed ID: 12714611; Miksch et al. 2005. PubMed ID: 16086317). In addition, several studies have reported a significantly increased risk of coronary artery disease in carriers of the ABCC6 p.Arg1141* variant (Trip et al. 2002. PubMed ID: 12176944; Köblös et al. 2010. PubMed ID: 19929409). Nonsense variants in ABCC6 are expected to be pathogenic. This variant is interpreted as pathogenic. -

Aug 30, 2022
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

PVS1, PS3, PM3_Strong -

Cutis laxa;C0332563:Papule Pathogenic:1
Oct 24, 2014
Centre for Mendelian Genomics, University Medical Centre Ljubljana
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

See cases Pathogenic:1
Apr 05, 2021
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

ACMG classification criteria: PVS1, PS3, PM3 -

Autosomal recessive inherited pseudoxanthoma elasticum;C1867450:Pseudoxanthoma elasticum, forme fruste;C3276161:Arterial calcification, generalized, of infancy, 2 Pathogenic:1
Oct 31, 2018
Fulgent Genetics, Fulgent Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.30
D
BayesDel_noAF
Pathogenic
0.58
CADD
Pathogenic
41
DANN
Uncertain
1.0
Eigen
Uncertain
0.67
Eigen_PC
Uncertain
0.50
FATHMM_MKL
Uncertain
0.90
D
Vest4
0.89
GERP RS
4.4

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs72653706; hg19: chr16-16256935; API