rs868239780

Variant names:

• chr20-36793674-C-A
• rs868239780
• NM_080627.4:c.4408G>T

Your query was ambiguous. Multiple possible variants found:

• chr20-36793674-C-A
• chr20-36793674-C-T

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.05

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]

ACMG classification

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
MTCL2	NM_080627.4	c.4408G>T	p.Gly1470Cys	missense_variant	Exon 14 of 15	ENST00000237536.9	NP_542194.2
MTCL2	NM_199181.3	c.2993+701G>T		intron_variant	Intron 14 of 14		NP_954650.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOGA1	ENST00000237536.9	c.4408G>T	p.Gly1470Cys	missense_variant	Exon 14 of 15	5	NM_080627.4	ENSP00000237536.4
SOGA1	ENST00000279034.10	c.2993+701G>T		intron_variant	Intron 14 of 14	5		ENSP00000279034.5
SOGA1	ENST00000465671.1	n.3247G>T		non_coding_transcript_exon_variant	Exon 10 of 12	2		ENSP00000433939.1

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

Other links and lift over

dbSNP: rs868239780; hg19: chr20-35422077;