rs964942007

Variant summary

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

The NM_080627.4(MTCL2):​c.4294C>T​(p.Arg1432Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000026 in 1,540,952 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R1432G) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

MTCL2
NM_080627.4 missense

Scores

5
8
3

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.66
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]

Genome browser will be placed here

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.4294C>T p.Arg1432Trp missense_variant Exon 14 of 15 ENST00000237536.9 NP_542194.2 O94964-2
MTCL2NM_199181.3 linkc.2993+587C>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.4294C>T p.Arg1432Trp missense_variant Exon 14 of 15 5 NM_080627.4 ENSP00000237536.4 O94964-2
SOGA1ENST00000279034.10 linkc.2993+587C>T intron_variant Intron 14 of 14 5 ENSP00000279034.5 X6R3R3
SOGA1ENST00000465671.1 linkn.3133C>T non_coding_transcript_exon_variant Exon 10 of 12 2 ENSP00000433939.1 H0YDM2

Frequencies

GnomAD3 genomes
AF:
0.0000131
AC:
2
AN:
152168
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000144
AC:
2
AN:
1388666
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
685282
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000185
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000131
AC:
2
AN:
152286
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.14
D
BayesDel_noAF
Uncertain
-0.040
CADD
Pathogenic
29
DANN
Pathogenic
1.0
Eigen
Uncertain
0.37
Eigen_PC
Uncertain
0.39
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Uncertain
0.97
D
M_CAP
Uncertain
0.12
D
MetaRNN
Uncertain
0.70
D
MetaSVM
Benign
-0.43
T
PrimateAI
Pathogenic
0.81
D
PROVEAN
Pathogenic
-6.0
D
REVEL
Benign
0.27
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Vest4
0.72
MutPred
0.32
Loss of MoRF binding (P = 0.0626);
MVP
0.37
MPC
2.3
ClinPred
1.0
D
GERP RS
3.7
gMVP
0.76

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: rs964942007; hg19: chr20-35422191; API