13-25257312-C-G

Variant summary

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

The NM_004685.5(MTMR6):​c.979G>C​(p.Val327Leu) 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. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

MTMR6
NM_004685.5 missense

Scores

19

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.597
Variant links:
Genes affected
MTMR6 (HGNC:7453): (myotubularin related protein 6) Enables phosphatidylinositol-3,5-bisphosphate phosphatase activity and phosphatidylinositol-3-phosphatase activity. Involved in phosphatidylinositol dephosphorylation. Located in cytoplasm and nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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=0.091245145).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MTMR6NM_004685.5 linkc.979G>C p.Val327Leu missense_variant Exon 9 of 14 ENST00000381801.6 NP_004676.3 Q9Y217-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MTMR6ENST00000381801.6 linkc.979G>C p.Val327Leu missense_variant Exon 9 of 14 1 NM_004685.5 ENSP00000371221.5 Q9Y217-1
MTMR6ENST00000482345.2 linkc.1093G>C p.Val365Leu missense_variant Exon 10 of 15 5 ENSP00000516657.1 A0A9L9PXJ0

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
33

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Dec 03, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.979G>C (p.V327L) alteration is located in exon 9 (coding exon 9) of the MTMR6 gene. This alteration results from a G to C substitution at nucleotide position 979, causing the valine (V) at amino acid position 327 to be replaced by a leucine (L). 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
0.10
BayesDel_addAF
Benign
-0.032
T
BayesDel_noAF
Benign
-0.28
CADD
Benign
9.0
DANN
Benign
0.88
DEOGEN2
Benign
0.31
T
Eigen
Benign
-0.90
Eigen_PC
Benign
-0.89
FATHMM_MKL
Benign
0.60
D
LIST_S2
Benign
0.69
T
M_CAP
Benign
0.043
D
MetaRNN
Benign
0.091
T
MetaSVM
Benign
-0.41
T
MutationAssessor
Benign
0.41
N
PrimateAI
Benign
0.34
T
PROVEAN
Benign
-0.97
N
REVEL
Benign
0.096
Sift
Benign
0.47
T
Sift4G
Benign
0.54
T
Polyphen
0.0
B
Vest4
0.17
MutPred
0.32
Gain of ubiquitination at K323 (P = 0.115);
MVP
0.67
MPC
0.12
ClinPred
0.025
T
GERP RS
2.7
Varity_R
0.085
gMVP
0.38

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr13-25831450; API