NM_016061.3:c.263C>T

Variant names:

• chr2-30158740-C-T
• NM_016061.3:c.263C>T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_016061.3(YPEL5):​c.263C>T​(p.Thr88Ile) 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 benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: YPEL5 NM_016061.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.70
• Publications: 0 publications found

Genes affected

YPEL5 (HGNC:18329): (yippee like 5) Predicted to enable metal ion binding activity. Predicted to be involved in cell population proliferation. Part of ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.4224688).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016061.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YPEL5	NM_016061.3	MANE Select	c.263C>T	p.Thr88Ile	missense	Exon 3 of 3	NP_057145.1	P62699
	YPEL5	NM_001127399.2		c.263C>T	p.Thr88Ile	missense	Exon 4 of 4	NP_001120871.1	P62699
	YPEL5	NM_001127400.2		c.263C>T	p.Thr88Ile	missense	Exon 4 of 4	NP_001120872.1	P62699

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YPEL5	ENST00000261353.9	TSL:1 MANE Select	c.263C>T	p.Thr88Ile	missense	Exon 3 of 3	ENSP00000261353.4	P62699
	YPEL5	ENST00000402708.5	TSL:1	c.263C>T	p.Thr88Ile	missense	Exon 4 of 4	ENSP00000385278.1	P62699
	YPEL5	ENST00000495673.1	TSL:1	n.537C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.57
BayesDel_addAF	Pathogenic	0.27	D
BayesDel_noAF	Pathogenic	0.16
CADD	Uncertain	24
DANN	Uncertain	0.98
DEOGEN2	Benign	0.044	T
Eigen	Uncertain	0.28
Eigen_PC	Uncertain	0.42
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.96	D
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.42	T
MetaSVM	Benign	-0.56	T
MutationAssessor	Uncertain	2.7	M
PhyloP100		7.7
PrimateAI	Pathogenic	0.87	D
PROVEAN	Benign	-1.2	N
REVEL	Uncertain	0.37
Sift	Benign	0.39	T
Sift4G	Benign	0.39	T
Polyphen		0.044	B
Vest4		0.64
MutPred		0.38		Loss of disorder (P = 0.0754)
MVP		0.26
MPC		1.6
ClinPred		0.88	D
GERP RS		5.6
Varity_R		0.56
gMVP		0.68
Mutation Taster		=40/60	disease causing

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

Other links and lift over

hg19: chr2-30381606;