rs72653762

chr16-16202006-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1 BP4_Moderate BS2

The NM_001171.6(ABCC6):c.1171A>G(p.Arg391Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00682 in 1,613,982 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0047 (4 hom., cov: 31)
  • Exomes 𝑓: 0.0070 (53 hom.)
• Consequence: ABCC6 NM_001171.6 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:8 B:1
• Conservation: PhyloP100: 0.705

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 4 uncertain in NM_001171.6
• BP4: Computational evidence support a benign effect (MetaRNN=0.080948204).
• BS2: High Homozygotes in GnomAd at 4 AD,AR,Digenic gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCC6	NM_001171.6	c.1171A>G	p.Arg391Gly	missense_variant	9/31	ENST00000205557.12
ABCC6	NM_001351800.1	c.829A>G	p.Arg277Gly	missense_variant	9/31
ABCC6	NR_147784.1	n.1208A>G		non_coding_transcript_exon_variant	9/29

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCC6	ENST00000205557.12	c.1171A>G	p.Arg391Gly	missense_variant	9/31	1	NM_001171.6	P1

Frequencies

GnomAD3 genomes AF: 0.00472 AC: 719 AN: 152216 Hom.: 4 Cov.: 31

Gnomad AFR AF: 0.00113

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00288

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00745

Gnomad FIN AF: 0.00433

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00791

Gnomad OTH AF: 0.00335

GnomAD3 exomes AF: 0.00557 AC: 1397 AN: 250940 Hom.: 5 AF XY: 0.00574 AC XY: 779 AN XY: 135674

Gnomad AFR exome AF: 0.00173

Gnomad AMR exome AF: 0.00298

Gnomad ASJ exome AF: 0.000199

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00768

Gnomad FIN exome AF: 0.00356

Gnomad NFE exome AF: 0.00805

Gnomad OTH exome AF: 0.00653

GnomAD4 exome AF: 0.00704 AC: 10284 AN: 1461648 Hom.: 53 Cov.: 32 AF XY: 0.00695 AC XY: 5052 AN XY: 727134

Gnomad4 AFR exome AF: 0.00120

Gnomad4 AMR exome AF: 0.00302

Gnomad4 ASJ exome AF: 0.000306

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00828

Gnomad4 FIN exome AF: 0.00504

Gnomad4 NFE exome AF: 0.00776

Gnomad4 OTH exome AF: 0.00730

GnomAD4 genome AF: 0.00471 AC: 718 AN: 152334 Hom.: 4 Cov.: 31 AF XY: 0.00432 AC XY: 322 AN XY: 74484

Gnomad4 AFR AF: 0.00113

Gnomad4 AMR AF: 0.00288

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00745

Gnomad4 FIN AF: 0.00433

Gnomad4 NFE AF: 0.00791

Gnomad4 OTH AF: 0.00331

Alfa AF: 0.00652 Hom.: 1

Bravo AF: 0.00479

ESP6500AA AF: 0.00182 AC: 8

ESP6500EA AF: 0.00919 AC: 79

ExAC AF: 0.00608 AC: 738

EpiCase AF: 0.00780

EpiControl AF: 0.00753

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:8 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:1 Uncertain:3 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 08, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 15, 2022	Recent study (not peer reviewed) including 590 probands with PXE showed a 2.9-fold enrichment of this variant among individuals with PXE versus population controls and incomplete penetrance, whereby only a small portion of probands with the p.(R391G) variant were symptomatic, but showed similar disease severity as probands with bi-allelic pathogenic loss-of-function variants (Szeri et al., 2020); Located in exon 9, a region with high sequence homology with an expressed pseudogene ABCC6P1; however, variant is not present in this pseudogene, which excludes the possibility that the high population frequency of p.(R391G) is due to a sequencing artifact; Arg391 residue is part of the 4th intracellular loop at the cytoplasmic surface of the protein and was suggested to have intramolecular interactions with several other residues and might be involved in the conformational switch of the protein (Szeri et al., 2020; Issa et al., 2020); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 15086542, 34440381, 32445016, 11702217, 28102862, 11536079, 16410789, 16086317, 24008425, 14631379, 16835894, 29722917, 17617515, 23485117, 28655553, 31398764, 32818659, 22209248, 29487417, 32039214, 34205333, 32873932, 26135620, 34426522, 32442430, 34148116, 33005041) -
Likely benign, criteria provided, single submitter	clinical testing	Invitae	Dec 31, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2024	- -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The ABCC6 p.Arg391Gly variant was identified in 10 of 852 proband chromosomes (frequency: 0.0117) from individuals with Pseudoxanthoma Elasticum (PXE) and Generalized Arterial Calcification of Infancy (GACI) (Nitschke_2012_PMID: 22209248; Chassaing_2004_PMID: 15086542; Pfendner_2007_PMID:17617515; Schulz_2006_PMID: 16835894; Miksch_2006_PMID:168358954). The R391G variant was also identified in 3 of 7 families affected with PXE, found in the compound heterozygous state. In two of these families the clinical manifestation of PXE was less severe, and one individual was asymptomatic but may not have presented with disease yet (Ringpfeil_2006_PMID:16410789). Therefore the R391G may contribute to a less severe form of the disorder. The variant was also identified in dbSNP (ID: rs72653762), LOVD 3.0 and ClinVar (classified as pathogenic by GeneDx and PXE International and as a VUS by EGL Genetics, Laboratory for Molecular Medicine, CeGaT Praxis fuer Humangenetik Tuebingen and Genomic Research Center, Shahid Beheshti University of Medical Sciences). The variant was identified in control databases in 1545 of 282338 chromosomes (5 homozygous) at a frequency of 0.005472 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant occurs outside of the splicing consensus sequence and 2 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. The variant was observed in the following populations: European (non-Finnish) in 1021 of 128772 chromosomes (freq: 0.007929), South Asian in 235 of 30614 chromosomes (freq: 0.007676), Other in 44 of 7218 chromosomes (freq: 0.006096), European (Finnish) in 95 of 25122 chromosomes (freq: 0.003782), Latino in 108 of 35440 chromosomes (freq: 0.003047), African in 40 of 24870 chromosomes (freq: 0.001608) and Ashkenazi Jewish in 2 of 10358 chromosomes (freq: 0.000193), while the variant was not observed in the East Asian population. The p.Arg391 residue is conserved in mammals but not in more distantly related organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -

not specified Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 28, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Reported in an individual with cutanous Pseudoxanthoma Elasticum who also had a multi exon deletion in ABCC6 (Chassing 2004). Also reported in two probands and in one affected twin sibling with generalized arterial calcification of infancy (Nitschke 2012), one of whom also had a frameshift variant. This was the only variant identified in the twins. MAF 0.8% with 3 homozygotes in ExAC. -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	May 19, 2023	Variant summary: ABCC6 c.1171A>G (p.Arg391Gly) results in a non-conservative amino acid change to a well-conserved residue (HGMD) located in a helix at the cytoplasmic site of transmembrane domain 1 (Szeri_2022) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0056 in 250940 control chromosomes in the gnomAD database, including 5 homozygotes. c.1171A>G has been reported in the literature in many individuals affected with Pseudoxanthoma Elasticum who are compound heterozygous with other pathogenic variants (e.g. Chassaing_2004, Garcia-Fernandez_2008, Ringpfeil_2006, Saeidan_2022, Schulz_2006, Szeri_2002). A modest enrichment in the frequency of the variant in affected individuals over the general population suggests the possibility that it may be associated with disease with a low penetrance, possibly mediated by interactions with unidentified variants in an interacting partner protein of ABCC6 (Szeri_2022). These reports do not provide unequivocal conclusions about association of the variant with Pseudoxanthoma Elasticum. At least two publications report experimental evidence evaluating an impact on protein function, finding no damaging effect of this variant on expression, subcellular localization, or functional activity (Szeri_2022, Saeidan_2022). The following publications have been ascertained in the context of this evaluation (PMID: 36317459, 15086542, 16410789, 16835894, 18513494, 16835894). Eight submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 with conflicting interpretations, and classified it as likely benign (n=2), pathogenic (n=1), and uncertain significance (n=5). Based on the evidence outlined above, the variant was classified as uncertain significance. -

Autosomal recessive inherited pseudoxanthoma elasticum Uncertain:2

Uncertain significance, no assertion criteria provided	research	PXE International	Mar 01, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genomic Research Center, Shahid Beheshti University of Medical Sciences	Aug 07, 2018	- -

ABCC6-related disorder Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 12, 2024

The ABCC6 c.1171A>G variant is predicted to result in the amino acid substitution p.Arg391Gly. This variant has been reported in the heterozygous, compound heterozygous, and homozygous states, as well as in the presence of other ABCC6 variants (phase not established), in individuals with pseudoxanthoma elasticum (PXE) of variable severity and onset (Chassaing et al. 2004. PubMed ID: 15086542; Misksch et al. 2005. PubMed ID: 16086317, Table 1; Ringpfeil et al. 2006. PubMed ID: 16410789, Figure 1; Schulz et al. 2006. PubMed ID: 16835894, Table 2; Pfendner et al. 2007. PubMed ID: 17617515, Table 2; Legrand et al. 2017. PubMed ID: 28102862; De Vilder et al. 2018. PubMed ID: 29722917, Table S3; Boraldi et al. 2020. PubMed ID: 32039214; Issa et al. 2020. PubMed ID: 32442430). It has been reported in the heterozygous state in the absence of a second variant in at least one individual from an ischemic stroke cohort (De Vilder et al. 2018. PubMed ID: 29722917, Table S3). It has been reported in the heterozygous state with and without the presence of a second ABCC6 variant (phase not established), in a limited number of individuals with generalized calcification of infancy (GACI) and/or vascular anomalies (Nitschke et al. 2012. PubMed ID: 22209248, Tables 2 and 3; Li et al. 2014. PubMed ID: 24008425, Table 2; Mattassi et al. 2018. PubMed ID: 28655553, Table II). A recent study reported this variant along with a second variant in 3 individuals with late onset PXE consisting of only ocular features with an onset of 80 years of age or older (Issa et al. 2020. PubMed ID: 32442430). This variant is thought to be a low penetrance hypomorphic allele capable of resulting in disease when combined with a severe pathogenic variant on the opposite allele (in trans) (Issa et al. 2020. PubMed ID: 32442430). More recently, the penetrance of this variant was hypothesized to be only 2%, however, when penetrant, it manifests a similar disease severity and progression to what two fully penetrant loss of function variants causes. In an updated version of gnomAD (v4), this variant has an allele frequency of 0.84% in individuals of Middle Eastern descent, including 57 homozygous individuals globally (https://gnomad.broadinstitute.org/variant/16-16202006-T-C?dataset=gnomad_r4), which is high for a primary disease causing variant. This variant is interpreted as likely pathogenic. -

Arterial calcification, generalized, of infancy, 2 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

MGZ Medical Genetics Center

Feb 14, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Uncertain	0.079	D
BayesDel_noAF	Pathogenic	0.35
Cadd	Benign	21
Dann	Uncertain	1.0
DEOGEN2	Uncertain	0.70	D;.
Eigen	Benign	0.12
Eigen_PC	Benign	-0.010
FATHMM_MKL	Uncertain	0.79	D
LIST_S2	Uncertain	0.93	D;D
M_CAP	Pathogenic	0.44	D
MetaRNN	Benign	0.081	T;T
MetaSVM	Uncertain	0.53	D
MutationAssessor	Uncertain	2.9	M;M
MutationTaster	Benign	1.0	D
PrimateAI	Benign	0.47	T
PROVEAN	Pathogenic	-6.6	D;.
REVEL	Pathogenic	0.85
Sift	Uncertain	0.0010	D;.
Sift4G	Uncertain	0.0020	D;D
Polyphen		1.0	D;.
Vest4		0.98
MVP		0.88
MPC		0.31
ClinPred		0.063	T
GERP RS		1.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.95
gMVP		0.68

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

Other links and lift over

dbSNP: rs72653762; hg19: chr16-16295863;