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
Consequence
NM_001171.6 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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ABCC6 | NM_001171.6 | c.3421C>T | p.Arg1141* | stop_gained | Exon 24 of 31 | ENST00000205557.12 | NP_001162.5 | |
ABCC6 | NM_001351800.1 | c.3079C>T | p.Arg1027* | stop_gained | Exon 24 of 31 | NP_001338729.1 | ||
ABCC6 | NR_147784.1 | n.3169-1514C>T | intron_variant | Intron 22 of 28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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ABCC6 | ENST00000205557.12 | c.3421C>T | p.Arg1141* | stop_gained | Exon 24 of 31 | 1 | NM_001171.6 | ENSP00000205557.7 | ||
ABCC6 | ENST00000622290.5 | n.3421C>T | non_coding_transcript_exon_variant | Exon 24 of 32 | 5 | ENSP00000483331.2 | ||||
ABCC6 | ENST00000456970.6 | n.*516-1514C>T | intron_variant | Intron 22 of 28 | 2 | ENSP00000405002.2 |
Frequencies
GnomAD3 genomes AF: 0.00113 AC: 172AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00141 AC: 355AN: 251296Hom.: 0 AF XY: 0.00154 AC XY: 209AN XY: 135858
GnomAD4 exome AF: 0.00166 AC: 2431AN: 1461600Hom.: 5 Cov.: 33 AF XY: 0.00171 AC XY: 1245AN XY: 727076
GnomAD4 genome AF: 0.00113 AC: 172AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.00107 AC XY: 80AN XY: 74490
ClinVar
Submissions by phenotype
not provided Pathogenic:13
ABCC6: PM3:Very Strong, PVS1, PP1:Strong, PM2:Supporting, PS3:Supporting -
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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) -
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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. -
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Autosomal recessive inherited pseudoxanthoma elasticum Pathogenic:10
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This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
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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 -
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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]. -
Criteria applied: PVS1,PM3_STR,PP4; Identified as compund heterozygous with NM_001171.6:c.3413G>A -
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Arterial calcification, generalized, of infancy, 2 Pathogenic:3
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This variant was classified as: Pathogenic. This variant was detected in homozygous state. -
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ABCC6-related disorder Pathogenic:2
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. -
PVS1, PS3, PM3_Strong -
Cutis laxa;C0332563:Papule Pathogenic:1
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See cases Pathogenic:1
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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at