chr3-51674407-G-A

Position:

• chr3-51674407-G-A

Variant summary

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

The NM_015926.6(TEX264):​c.103G>A​(p.Glu35Lys) 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: TEX264 NM_015926.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

Genes affected

TEX264 (HGNC:30247): (testis expressed 264, ER-phagy receptor) Enables signaling receptor activity. Involved in protein-DNA covalent cross-linking repair. Acts upstream of or within reticulophagy. Located in several cellular components, including autophagosome membrane; endoplasmic reticulum membrane; and replication fork. [provided by Alliance of Genome Resources, Apr 2022]

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=0.13036487).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX264	NM_015926.6	c.103G>A	p.Glu35Lys	missense_variant	2/5	ENST00000341333.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX264	ENST00000341333.10	c.103G>A	p.Glu35Lys	missense_variant	2/5	1	NM_015926.6	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.081
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	14
DANN	Benign	0.86
DEOGEN2	Benign	0.020	T;.;T;T;T;.;T;T;T;T;T;.
Eigen	Benign	-0.64
Eigen_PC	Benign	-0.49
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Benign	0.72	T;T;.;T;.;T;T;.;.;.;T;T
M_CAP	Benign	0.011	T
MetaRNN	Benign	0.13	T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.89	T
MutationTaster	Benign	1.0	N;N;N;N;N
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-1.0	N;.;N;.;N;N;N;N;N;N;N;N
REVEL	Benign	0.12
Sift	Benign	0.73	T;.;T;.;T;T;T;T;T;T;T;T
Sift4G	Benign	0.061	T;T;T;T;T;T;T;T;T;T;T;T
Polyphen		0.0010	.;.;B;B;B;.;.;B;B;B;.;.
Vest4		0.22, 0.13, 0.13
MutPred		0.37		Gain of ubiquitination at E35 (P = 0.0219);Gain of ubiquitination at E35 (P = 0.0219);Gain of ubiquitination at E35 (P = 0.0219);Gain of ubiquitination at E35 (P = 0.0219);Gain of ubiquitination at E35 (P = 0.0219);Gain of ubiquitination at E35 (P = 0.0219);Gain of ubiquitination at E35 (P = 0.0219);Gain of ubiquitination at E35 (P = 0.0219);Gain of ubiquitination at E35 (P = 0.0219);Gain of ubiquitination at E35 (P = 0.0219);Gain of ubiquitination at E35 (P = 0.0219);Gain of ubiquitination at E35 (P = 0.0219);
MVP		0.043
MPC		0.32
ClinPred		0.035	T
GERP RS		-0.018
Varity_R		0.026
gMVP		0.55

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: chr3-51708423;