17-58561571-T-G

Position:

• chr17-58561571-T-G

Variant summary

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

The NM_031272.5(TEX14):​c.4106A>C​(p.Gln1369Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: TEX14 NM_031272.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.99

Genes affected

TEX14 (HGNC:11737): (testis expressed 14, intercellular bridge forming factor) The protein encoded by this gene is necessary for intercellular bridges in germ cells, which are required for spermatogenesis. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2011]

ACMG classification

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	UniProt
TEX14	NM_031272.5	c.4106A>C	p.Gln1369Pro	missense_variant	29/32	ENST00000349033.10
TEX14	NM_001201457.2	c.4244A>C	p.Gln1415Pro	missense_variant	30/33
TEX14	NM_198393.4	c.4226A>C	p.Gln1409Pro	missense_variant	30/33

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX14	ENST00000349033.10	c.4106A>C	p.Gln1369Pro	missense_variant	29/32	5	NM_031272.5	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Non-obstructive azoospermia Uncertain:1

Uncertain significance, criteria provided, single submitter

research

Institute of Reproductive Genetics, University of Münster

Aug 23, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.067	T
BayesDel_noAF	Benign	-0.33
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.14	.;T;.
Eigen	Uncertain	0.47
Eigen_PC	Uncertain	0.42
FATHMM_MKL	Uncertain	0.81	D
LIST_S2	Benign	0.79	T;T;T
M_CAP	Benign	0.0085	T
MetaRNN	Uncertain	0.57	D;D;D
MetaSVM	Benign	-0.93	T
MutationAssessor	Benign	1.6	.;L;.
MutationTaster	Benign	0.88	N;N;N
PrimateAI	Benign	0.31	T
PROVEAN	Uncertain	-2.7	D;D;D
REVEL	Benign	0.10
Sift	Uncertain	0.0010	D;D;D
Sift4G	Benign	0.20	T;T;T
Polyphen		1.0	D;D;D
Vest4		0.54
MutPred		0.23		.;Gain of catalytic residue at Q1415 (P = 0.0053);.;
MVP		0.46
MPC		0.35
ClinPred		0.97	D
GERP RS		4.0
Varity_R		0.37
gMVP		0.043

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: chr17-56638932;