Variant 20-36793788-G-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_080627.4(SOGA1):c.4294C>G(p.Arg1432Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000288 in 1,388,666 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000029 ( 0 hom. )

Consequence

SOGA1
NM_080627.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.66

Variant links:

Genes affected

SOGA1 (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]

SOGA1 links:

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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/exons	MANE	Protein	UniProt
SOGA1	NM_080627.4 linkuse as main transcript	c.4294C>G	p.Arg1432Gly	missense_variant	14/15	ENST00000237536.9	NP_542194.2
SOGA1	NM_199181.3 linkuse as main transcript	c.2993+587C>G		intron_variant			NP_954650.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOGA1	ENST00000237536.9 linkuse as main transcript	c.4294C>G	p.Arg1432Gly	missense_variant	14/15	5	NM_080627.4	ENSP00000237536	P2	O94964-2
SOGA1	ENST00000279034.10 linkuse as main transcript	c.2993+587C>G		intron_variant		5		ENSP00000279034	A2
SOGA1	ENST00000465671.1 linkuse as main transcript	c.3136C>G	p.Arg1046Gly	missense_variant, NMD_transcript_variant	10/12	2		ENSP00000433939

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000692

AC:

AN:

144556

Hom.:

AF XY:

0.0000129

AC XY:

AN XY:

77558

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000172

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000288

AC:

AN:

1388666

Hom.:

Cov.:

AF XY:

0.00000438

AC XY:

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:

0.00000371

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 04, 2024

The c.4294C>G (p.R1432G) alteration is located in exon 14 (coding exon 14) of the SOGA1 gene. This alteration results from a C to G substitution at nucleotide position 4294, causing the arginine (R) at amino acid position 1432 to be replaced by a glycine (G). 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

BayesDel_addAF

Uncertain

0.12

BayesDel_noAF

Uncertain

-0.060

CADD

Uncertain

DANN

Uncertain

1.0

Eigen

Uncertain

0.37

Eigen_PC

Uncertain

0.39

FATHMM_MKL

Uncertain

0.93

LIST_S2

Uncertain

0.93

M_CAP

Uncertain

0.14

MetaRNN

Uncertain

0.63

MetaSVM

Benign

-0.43

MutationTaster

Benign

1.0

D;D;D;D

PrimateAI

Uncertain

0.75

PROVEAN

Pathogenic

-5.3

REVEL

Benign

0.25

Sift

Uncertain

0.0020

Sift4G

Pathogenic

0.0

Vest4

0.76

MutPred

0.28

Loss of MoRF binding (P = 0.0156);

MVP

0.082

MPC

2.5

ClinPred

0.99

GERP RS

3.7

gMVP

0.80

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over