rs868239780

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_080627.4(MTCL2):​c.4408G>T​(p.Gly1470Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1470S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

MTCL2
NM_080627.4 missense

Scores

1
8
7

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.05
Variant links:
Genes affected
MTCL2 (HGNC:16111): (microtubule crosslinking factor 2) Predicted to be involved in insulin receptor signaling pathway; negative regulation of gluconeogenesis; and regulation of autophagy. Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MTCL2NM_080627.4 linkc.4408G>T p.Gly1470Cys missense_variant Exon 14 of 15 ENST00000237536.9 NP_542194.2 O94964-2
MTCL2NM_199181.3 linkc.2993+701G>T intron_variant Intron 14 of 14 NP_954650.2 O94964X6R3R3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SOGA1ENST00000237536.9 linkc.4408G>T p.Gly1470Cys missense_variant Exon 14 of 15 5 NM_080627.4 ENSP00000237536.4 O94964-2
SOGA1ENST00000279034.10 linkc.2993+701G>T intron_variant Intron 14 of 14 5 ENSP00000279034.5 X6R3R3
SOGA1ENST00000465671.1 linkn.3247G>T non_coding_transcript_exon_variant Exon 10 of 12 2 ENSP00000433939.1 H0YDM2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.15
D
BayesDel_noAF
Uncertain
-0.030
CADD
Pathogenic
27
DANN
Uncertain
0.99
Eigen
Benign
-0.018
Eigen_PC
Benign
-0.032
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.89
D
M_CAP
Benign
0.057
D
MetaRNN
Uncertain
0.49
T
MetaSVM
Benign
-1.1
T
PrimateAI
Uncertain
0.75
T
PROVEAN
Uncertain
-3.6
D
REVEL
Uncertain
0.29
Sift
Benign
0.034
D
Sift4G
Benign
0.066
T
Vest4
0.75
MutPred
0.28
Loss of ubiquitination at K1467 (P = 0.0551);
MVP
0.12
MPC
2.3
ClinPred
0.97
D
GERP RS
3.9
gMVP
0.42

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: rs868239780; hg19: chr20-35422077; API