X-70529854-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_031276.3(TEX11):c.2666A>G(p.Lys889Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 22)
• Consequence: TEX11 NM_031276.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.22

Genes affected

TEX11 (HGNC:11733): (testis expressed 11) This gene is X-linked and is expressed in only male germ cells. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14250419).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX11	NM_031276.3	c.2666A>G	p.Lys889Arg	missense_variant	29/30	ENST00000374333.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX11	ENST00000374333.7	c.2666A>G	p.Lys889Arg	missense_variant	29/30	1	NM_031276.3	P2
TEX11	ENST00000344304.3	c.2711A>G	p.Lys904Arg	missense_variant	28/29	5		A2
TEX11	ENST00000395889.6	c.2711A>G	p.Lys904Arg	missense_variant	30/31	2		A2
TEX11	ENST00000374320.6	c.1736A>G	p.Lys579Arg	missense_variant	18/19	2

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 22

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

TEX11: PM2, BP4 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.070
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.79
Cadd	Benign	13
Dann	Uncertain	0.99
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Benign	0.76	T;T;T;.
M_CAP	Benign	0.0065	T
MetaRNN	Benign	0.14	T;T;T;T
MetaSVM	Benign	-1.1	T
MutationTaster	Benign	0.95	N;N;N;N
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-1.2	N;N;N;N
REVEL	Benign	0.068
Sift	Benign	0.089	T;T;T;T
Sift4G	Benign	0.073	T;T;T;T
Polyphen		0.70	P;.;P;P
Vest4		0.086
MutPred		0.38		.;.;Loss of ubiquitination at K904 (P = 0.0087);Loss of ubiquitination at K904 (P = 0.0087);
MVP		0.34
MPC		0.49
ClinPred		0.73	D
GERP RS		3.2
Varity_R		0.087
gMVP		0.13

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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.

Other links and lift over

hg19: chrX-69749704;