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GeneBe

16-16212228-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001171.6(ABCC6):c.619G>A(p.Gly207Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 22)

Consequence

ABCC6
NM_001171.6 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.22
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 Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2225776).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ABCC6NM_001171.6 linkuse as main transcriptc.619G>A p.Gly207Arg missense_variant 6/31 ENST00000205557.12
LOC105371100XR_933131.3 linkuse as main transcriptn.282+137C>T intron_variant, non_coding_transcript_variant
ABCC6NM_001351800.1 linkuse as main transcriptc.277G>A p.Gly93Arg missense_variant 6/31
ABCC6NR_147784.1 linkuse as main transcriptn.656G>A non_coding_transcript_exon_variant 6/29

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ABCC6ENST00000205557.12 linkuse as main transcriptc.619G>A p.Gly207Arg missense_variant 6/311 NM_001171.6 P1O95255-1

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD4 exome
Cov.:
11
GnomAD4 genome
Cov.:
22

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Autosomal recessive inherited pseudoxanthoma elasticum Uncertain:1
Uncertain significance, criteria provided, single submitterresearchPXE InternationalFeb 16, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Uncertain
0.046
T
BayesDel_noAF
Benign
-0.17
Cadd
Benign
18
Dann
Benign
0.97
DEOGEN2
Benign
0.093
T;.
Eigen
Benign
-0.63
Eigen_PC
Benign
-0.56
FATHMM_MKL
Benign
0.26
N
LIST_S2
Benign
0.71
T;T
M_CAP
Benign
0.066
D
MetaRNN
Benign
0.22
T;T
MetaSVM
Benign
-0.59
T
MutationAssessor
Benign
1.8
L;L
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.40
T
PROVEAN
Benign
-1.9
N;.
REVEL
Uncertain
0.31
Sift
Benign
0.18
T;.
Sift4G
Benign
0.33
T;T
Polyphen
0.0090
B;.
Vest4
0.16
MutPred
0.27
Gain of glycosylation at T206 (P = 0.0603);Gain of glycosylation at T206 (P = 0.0603);
MVP
0.72
MPC
1.5
ClinPred
0.38
T
GERP RS
2.9
Varity_R
0.076
gMVP
0.36

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.080
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: rs72657697; hg19: chr16-16306085; API