6-112054360-G-T

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate

The NM_198239.2(CCN6):​c.3G>T​(p.Met1?) variant causes a start lost change. The variant allele was found at a frequency of 0.0000157 in 1,461,886 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.000016 ( 0 hom. )

Consequence

CCN6
NM_198239.2 start_lost

Scores

5
6
6

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 6.64
Variant links:
Genes affected
CCN6 (HGNC:12771): (cellular communication network factor 6) This gene encodes a member of the WNT1 inducible signaling pathway (WISP) protein subfamily, which belongs to the connective tissue growth factor (CTGF) family. WNT1 is a member of a family of cysteine-rich, glycosylated signaling proteins that mediate diverse developmental processes. The CTGF family members are characterized by four conserved cysteine-rich domains: insulin-like growth factor-binding domain, von Willebrand factor type C module, thrombospondin domain and C-terminal cystine knot-like domain. This gene is overexpressed in colon tumors. It may be downstream in the WNT1 signaling pathway that is relevant to malignant transformation. Mutations of this gene are associated with progressive pseudorheumatoid dysplasia, an autosomal recessive skeletal disorder, indicating that the gene is essential for normal postnatal skeletal growth and cartilage homeostasis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PVS1
Start lost variant, next in-frame start position is after 18 pathogenic variants. Next in-frame start position is after 582 CDS bases. Genomic position: 112064990. Lost 0.546 part of the original CDS.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 6-112054360-G-T is Pathogenic according to our data. Variant chr6-112054360-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 2902108.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCN6NM_198239.2 linkc.3G>T p.Met1? start_lost Exon 1 of 5 ENST00000368666.7 NP_937882.2 O95389-1A0A384NYW3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCN6ENST00000368666.7 linkc.3G>T p.Met1? start_lost Exon 1 of 5 1 NM_198239.2 ENSP00000357655.4 O95389-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251474
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135914
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000879
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000157
AC:
23
AN:
1461886
Hom.:
0
Cov.:
31
AF XY:
0.0000179
AC XY:
13
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000207
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00
AC:
0

ClinVar

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

Submissions by phenotype

not provided Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 05, 2023For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the WISP3 protein in which other variant(s) (p.Cys114Trp) have been determined to be pathogenic (PMID: 21993478, 22685593, 25553839, 25738435, 28018607). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This variant has not been reported in the literature in individuals affected with WISP3-related conditions. This variant is present in population databases (rs782220219, gnomAD 0.0009%). This sequence change affects the initiator methionine of the WISP3 mRNA. The next in-frame methionine is located at codon 195. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.63
D
BayesDel_noAF
Uncertain
0.040
CADD
Benign
22
DANN
Uncertain
0.98
DEOGEN2
Benign
0.12
.;T;T;T
Eigen
Uncertain
0.54
Eigen_PC
Uncertain
0.48
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.54
T;D;.;.
M_CAP
Pathogenic
0.63
D
MetaRNN
Pathogenic
0.99
D;D;D;D
MetaSVM
Benign
-0.35
T
PrimateAI
Uncertain
0.54
T
PROVEAN
Benign
-1.0
.;N;.;N
REVEL
Uncertain
0.54
Sift
Pathogenic
0.0
.;D;.;D
Sift4G
Benign
0.28
T;T;T;T
Polyphen
0.99
D;D;D;D
Vest4
0.56
MutPred
0.98
.;Gain of catalytic residue at M1 (P = 0.0107);Gain of catalytic residue at M1 (P = 0.0107);Gain of catalytic residue at M1 (P = 0.0107);
MVP
0.81
MPC
0.11
ClinPred
0.99
D
GERP RS
5.0
Varity_R
0.89
gMVP
0.53

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: rs782220219; hg19: chr6-112375563; API