10-102918516-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate

The NM_017649.5(CNNM2):​c.36G>T​(p.Lys12Asn) 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. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

CNNM2
NM_017649.5 missense

Scores

3
1
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.34
Variant links:
Genes affected
CNNM2 (HGNC:103): (cyclin and CBS domain divalent metal cation transport mediator 2) This gene encodes a member of the ancient conserved domain containing protein family. Members of this protein family contain a cyclin box motif and have structural similarity to the cyclins. The encoded protein may play an important role in magnesium homeostasis by mediating the epithelial transport and renal reabsorption of Mg2+. Mutations in this gene are associated with renal hypomagnesemia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in the CNNM2 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 16 curated pathogenic missense variants (we use a threshold of 10). The gene has 10 curated benign missense variants. Gene score misZ: 4.4105 (above the threshold of 3.09). Trascript score misZ: 5.0056 (above the threshold of 3.09). GenCC associations: The gene is linked to hypomagnesemia, seizures, and intellectual disability 1, familial primary hypomagnesemia with normocalciuria and normocalcemia, renal hypomagnesemia 6.
BP4
Computational evidence support a benign effect (MetaRNN=0.21850157).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CNNM2NM_017649.5 linkc.36G>T p.Lys12Asn missense_variant Exon 1 of 8 ENST00000369878.9 NP_060119.3 Q9H8M5-1
CNNM2NM_199076.3 linkc.36G>T p.Lys12Asn missense_variant Exon 1 of 7 NP_951058.1 Q9H8M5-2
CNNM2NM_199077.3 linkc.36G>T p.Lys12Asn missense_variant Exon 1 of 2 NP_951059.1 Q9H8M5-3
LOC107984265NR_160733.1 linkn.-181C>A upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CNNM2ENST00000369878.9 linkc.36G>T p.Lys12Asn missense_variant Exon 1 of 8 1 NM_017649.5 ENSP00000358894.3 Q9H8M5-1
CNNM2ENST00000369875.3 linkc.36G>T p.Lys12Asn missense_variant Exon 1 of 2 1 ENSP00000358891.3 Q9H8M5-3
CNNM2ENST00000433628.2 linkc.36G>T p.Lys12Asn missense_variant Exon 1 of 7 2 ENSP00000392875.2 Q9H8M5-2
ENSG00000286575ENST00000652934.1 linkn.-181C>A upstream_gene_variant

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Aug 27, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.36G>T (p.K12N) alteration is located in exon 1 (coding exon 1) of the CNNM2 gene. This alteration results from a G to T substitution at nucleotide position 36, causing the lysine (K) at amino acid position 12 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.25
BayesDel_addAF
Benign
-0.044
T
BayesDel_noAF
Benign
-0.30
CADD
Benign
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.017
T;.;.
Eigen
Benign
-0.095
Eigen_PC
Benign
0.027
FATHMM_MKL
Benign
0.076
N
LIST_S2
Benign
0.68
T;T;T
M_CAP
Pathogenic
0.91
D
MetaRNN
Benign
0.22
T;T;T
MetaSVM
Benign
-0.63
T
MutationAssessor
Benign
0.0
N;N;N
PrimateAI
Pathogenic
0.95
D
PROVEAN
Benign
-0.28
N;N;N
REVEL
Benign
0.21
Sift
Benign
0.077
T;T;T
Sift4G
Pathogenic
0.0
D;D;D
Polyphen
0.18
B;.;B
Vest4
0.12
MutPred
0.28
Loss of ubiquitination at K12 (P = 0.0118);Loss of ubiquitination at K12 (P = 0.0118);Loss of ubiquitination at K12 (P = 0.0118);
MVP
0.043
ClinPred
0.50
T
GERP RS
4.0
Varity_R
0.20
gMVP
0.62

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-104678273; API