Variant X-135158271-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5

The NM_001031705.3(CT55):c.465T>A(p.Tyr155Ter) variant causes a stop gained change involving the alteration of a non-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 Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 22)

Consequence

CT55
NM_001031705.3 stop_gained

Scores

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 0.693

Variant links:

Genes affected

CT55 (HGNC:26047): (cancer/testis antigen 55)

CT55 links:

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 11 ACMG points.

PVS1

Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant X-135158271-A-T is Pathogenic according to our data. Variant chrX-135158271-A-T is described in ClinVar as [Pathogenic]. Clinvar id is 2499997.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CT55	NM_001031705.3 linkuse as main transcript	c.465T>A	p.Tyr155Ter	stop_gained	4/6	ENST00000276241.11	NP_001026875.1
CT55	NM_017863.2 linkuse as main transcript	c.465T>A	p.Tyr155Ter	stop_gained	4/5		NP_060333.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CT55	ENST00000276241.11 linkuse as main transcript	c.465T>A	p.Tyr155Ter	stop_gained	4/6	1	NM_001031705.3	ENSP00000276241	A2	Q8WUE5-1
CT55	ENST00000344129.2 linkuse as main transcript	c.465T>A	p.Tyr155Ter	stop_gained	4/5	1		ENSP00000343893	P2	Q8WUE5-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Spermatogenic failure, X-linked, 7

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Sep 27, 2023

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.19

BayesDel_noAF

Uncertain

0.030

CADD

Benign

DANN

Benign

0.96

FATHMM_MKL

Benign

0.027

MutationTaster

Benign

1.0

A;A

Vest4

0.036

GERP RS

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over