2-218488414-C-T

Position:

• chr2-218488414-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_020935.3(USP37):​c.1480G>A​(p.Glu494Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: USP37 NM_020935.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.80

Genes affected

USP37 (HGNC:20063): (ubiquitin specific peptidase 37) Enables cysteine-type endopeptidase activity; protein kinase binding activity; and thiol-dependent deubiquitinase. Involved in G1/S transition of mitotic cell cycle; protein deubiquitination; and regulation of DNA replication. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.798

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
USP37	NM_020935.3	c.1480G>A	p.Glu494Lys	missense_variant	15/26	ENST00000258399.8	NP_065986.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
USP37	ENST00000258399.8	c.1480G>A	p.Glu494Lys	missense_variant	15/26	1	NM_020935.3	ENSP00000258399.3
USP37	ENST00000418019.5	c.1480G>A	p.Glu494Lys	missense_variant	15/26	1		ENSP00000396585.1
USP37	ENST00000415516.5	c.1264G>A	p.Glu422Lys	missense_variant	14/24	1		ENSP00000400902.1
USP37	ENST00000454775.5	c.1480G>A	p.Glu494Lys	missense_variant	15/26	2		ENSP00000393662.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 31

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2023

USP37: PM2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.85
BayesDel_addAF	Pathogenic	0.18	D
BayesDel_noAF	Uncertain	0.020
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Benign	0.0088	T;T;.;T
Eigen	Uncertain	0.59
Eigen_PC	Uncertain	0.66
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.95	.;.;D;D
M_CAP	Benign	0.025	D
MetaRNN	Pathogenic	0.80	D;D;D;D
MetaSVM	Benign	-0.93	T
MutationAssessor	Uncertain	2.5	M;M;.;M
PrimateAI	Uncertain	0.70	T
PROVEAN	Benign	-2.1	N;N;N;N
REVEL	Uncertain	0.33
Sift	Benign	0.053	T;T;T;T
Sift4G	Benign	0.084	T;T;T;T
Polyphen		1.0	D;D;D;D
Vest4		0.81
MutPred		0.56		Gain of methylation at E494 (P = 0.0071);Gain of methylation at E494 (P = 0.0071);.;Gain of methylation at E494 (P = 0.0071);
MVP		0.24
MPC		1.1
ClinPred		0.96	D
GERP RS		5.4
Varity_R		0.30
gMVP		0.56

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: rs780297000; hg19: chr2-219353137;