rs144223596

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2

The ENST00000295550.9(COL6A3):​c.4510C>T​(p.Arg1504Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000876 in 1,614,116 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. R1504R) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00062 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00090 ( 2 hom. )

Consequence

COL6A3
ENST00000295550.9 missense

Scores

3
13
3

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:6B:2

Conservation

PhyloP100: 3.27
Variant links:
Genes affected
COL6A3 (HGNC:2213): (collagen type VI alpha 3 chain) This gene encodes the alpha-3 chain, one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The alpha-3 chain of type VI collagen is much larger than the alpha-1 and -2 chains. This difference in size is largely due to an increase in the number of subdomains, similar to von Willebrand Factor type A domains, that are found in the amino terminal globular domain of all the alpha chains. These domains have been shown to bind extracellular matrix proteins, an interaction that explains the importance of this collagen in organizing matrix components. Mutations in the type VI collagen genes are associated with Bethlem myopathy, a rare autosomal dominant proximal myopathy with early childhood onset. Mutations in this gene are also a cause of Ullrich congenital muscular dystrophy, also referred to as Ullrich scleroatonic muscular dystrophy, an autosomal recessive congenital myopathy that is more severe than Bethlem myopathy. Multiple transcript variants have been identified, but the full-length nature of only some of these variants has been described. [provided by RefSeq, Jun 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP6
Variant 2-237368953-G-A is Benign according to our data. Variant chr2-237368953-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 166943.We mark this variant Likely_benign, oryginal submissions are: {Benign=1, Uncertain_significance=6, Likely_benign=1}.
BS2
High Homozygotes in GnomAdExome4 at 2 SD gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COL6A3NM_004369.4 linkuse as main transcriptc.4510C>T p.Arg1504Trp missense_variant 10/44 ENST00000295550.9 NP_004360.2
COL6A3NM_057167.4 linkuse as main transcriptc.3892C>T p.Arg1298Trp missense_variant 9/43 NP_476508.2
COL6A3NM_057166.5 linkuse as main transcriptc.2689C>T p.Arg897Trp missense_variant 7/41 NP_476507.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
COL6A3ENST00000295550.9 linkuse as main transcriptc.4510C>T p.Arg1504Trp missense_variant 10/441 NM_004369.4 ENSP00000295550 P1P12111-1
COL6A3ENST00000472056.5 linkuse as main transcriptc.2689C>T p.Arg897Trp missense_variant 7/411 ENSP00000418285 P12111-4
COL6A3ENST00000353578.9 linkuse as main transcriptc.3892C>T p.Arg1298Trp missense_variant 9/435 ENSP00000315873 P12111-2
COL6A3ENST00000684597.1 linkuse as main transcriptc.117-277C>T intron_variant ENSP00000508021

Frequencies

GnomAD3 genomes
AF:
0.000618
AC:
94
AN:
152222
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000965
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00259
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00110
Gnomad OTH
AF:
0.000955
GnomAD3 exomes
AF:
0.000434
AC:
109
AN:
251426
Hom.:
0
AF XY:
0.000434
AC XY:
59
AN XY:
135894
show subpopulations
Gnomad AFR exome
AF:
0.000123
Gnomad AMR exome
AF:
0.000318
Gnomad ASJ exome
AF:
0.00109
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000677
Gnomad OTH exome
AF:
0.000978
GnomAD4 exome
AF:
0.000903
AC:
1320
AN:
1461894
Hom.:
2
Cov.:
38
AF XY:
0.000844
AC XY:
614
AN XY:
727248
show subpopulations
Gnomad4 AFR exome
AF:
0.000119
Gnomad4 AMR exome
AF:
0.000291
Gnomad4 ASJ exome
AF:
0.00172
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.0000562
Gnomad4 NFE exome
AF:
0.00106
Gnomad4 OTH exome
AF:
0.00116
GnomAD4 genome
AF:
0.000618
AC:
94
AN:
152222
Hom.:
0
Cov.:
33
AF XY:
0.000565
AC XY:
42
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.0000965
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00259
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00110
Gnomad4 OTH
AF:
0.000955
Alfa
AF:
0.000823
Hom.:
1
Bravo
AF:
0.000593
TwinsUK
AF:
0.00108
AC:
4
ALSPAC
AF:
0.00104
AC:
4
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000465
AC:
4
ExAC
AF:
0.000329
AC:
40
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.000600
EpiControl
AF:
0.00107

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:6Benign:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:5
Uncertain significance, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2024- -
Uncertain significance, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Mar 15, 2018- -
Uncertain significance, criteria provided, single submitterclinical testingAthena DiagnosticsJun 03, 2019- -
Uncertain significance, criteria provided, single submitterclinical testingRevvity Omics, RevvityMar 18, 2023- -
Uncertain significance, criteria provided, single submitterclinical testingGeneDxJul 05, 2022Reported previously in the heterozygous state as a variant of uncertain significance in an individual with limb-girdle muscular dystrophy (Nallamilli et al., 2018); Reported along with a second COL6A3 variant in a patient with segmental and cervical dystonia and tremor; however, segregation information was not available (Kumar et al., 2019); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29411265, 30564623, 31731261) -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpApr 29, 2024Variant summary: COL6A3 c.4510C>T (p.Arg1504Trp) results in a non-conservative amino acid change located in the von Willebrand factor, type A domain (IPR002035) 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 0.00088 in 1614116 control chromosomes in the gnomAD database, including 2 homozygotes. c.4510C>T has been reported in the literature in individuals affected with clinical features of COL6A3-related conditions (e.g. Kumar_2019, Meinke_2020, Nallamilli_2018). These reports do not provide unequivocal conclusions about association of the variant with Ullrich Congenital Muscular Dystrophy 1. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 31731261, 31862442, 30564623). ClinVar contains an entry for this variant (Variation ID: 166943). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Collagen 6-related myopathy Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 25, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.29
BayesDel_addAF
Benign
-0.060
T
BayesDel_noAF
Uncertain
0.070
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.60
.;D;.;T;.
Eigen
Uncertain
0.57
Eigen_PC
Uncertain
0.40
FATHMM_MKL
Uncertain
0.82
D
LIST_S2
Pathogenic
0.98
D;D;D;D;.
M_CAP
Uncertain
0.25
D
MetaRNN
Uncertain
0.65
D;D;D;D;D
MetaSVM
Uncertain
0.77
D
MutationAssessor
Pathogenic
3.6
.;H;.;.;.
MutationTaster
Benign
0.99
D;D;D;D;D;D
PrimateAI
Uncertain
0.52
T
PROVEAN
Uncertain
-4.2
D;D;D;.;D
REVEL
Uncertain
0.58
Sift
Uncertain
0.014
D;D;D;.;D
Sift4G
Pathogenic
0.0
D;D;D;D;D
Polyphen
1.0
D;D;.;.;D
Vest4
0.77
MVP
0.96
MPC
0.66
ClinPred
0.22
T
GERP RS
5.4
Varity_R
0.54
gMVP
0.75

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: rs144223596; hg19: chr2-238277596; COSMIC: COSV55089488; COSMIC: COSV55089488; API