11-61008546-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_006725.5(CD6):c.482T>G(p.Leu161Arg) variant causes a missense change. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CD6
NM_006725.5 missense
NM_006725.5 missense
Scores
7
9
3
Clinical Significance
Conservation
PhyloP100: 5.71
Genes affected
CD6 (HGNC:1691): (CD6 molecule) This gene encodes a protein found on the outer membrane of T-lymphocytes as well as some other immune cells. The encoded protein contains three scavenger receptor cysteine-rich (SRCR) domains and a binding site for an activated leukocyte cell adhesion molecule. The gene product is important for continuation of T cell activation. This gene may be associated with susceptibility to multiple sclerosis (PMID: 19525953, 21849685). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.847
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD6 | NM_006725.5 | c.482T>G | p.Leu161Arg | missense_variant | 4/13 | ENST00000313421.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD6 | ENST00000313421.11 | c.482T>G | p.Leu161Arg | missense_variant | 4/13 | 1 | NM_006725.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 5AN: 151614Hom.: 0 Cov.: 33 FAILED QC
GnomAD3 genomes
?
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33
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000207 AC: 3AN: 1446444Hom.: 0 Cov.: 29 AF XY: 0.00000278 AC XY: 2AN XY: 718390
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000330 AC: 5AN: 151614Hom.: 0 Cov.: 33 AF XY: 0.0000540 AC XY: 4AN XY: 74020
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2023 | The c.482T>G (p.L161R) alteration is located in exon 4 (coding exon 4) of the CD6 gene. This alteration results from a T to G substitution at nucleotide position 482, causing the leucine (L) at amino acid position 161 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;T;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
H;.;.;H;H
MutationTaster
Benign
N;N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D;D;D
Sift4G
Pathogenic
D;D;D;D;D
Polyphen
D;.;D;D;D
Vest4
MutPred
Loss of stability (P = 0.0041);Loss of stability (P = 0.0041);Loss of stability (P = 0.0041);Loss of stability (P = 0.0041);Loss of stability (P = 0.0041);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.