7-98217783-C-T

Variant summary

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

The NM_015395.3(TECPR1):​c.3293G>A​(p.Gly1098Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,550,946 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000085 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000079 ( 0 hom. )

Consequence

TECPR1
NM_015395.3 missense

Scores

1
14
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.84
Variant links:
Genes affected
TECPR1 (HGNC:22214): (tectonin beta-propeller repeat containing 1) This gene encodes a tethering factor involved in autophagy. The encoded protein is found at autolysosomes, and is involved in targeting protein aggregates, damaged mitochondria, and bacterial pathogens for autophagy [provided by RefSeq, Nov 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 rank MANE Protein UniProt
TECPR1NM_015395.3 linkc.3293G>A p.Gly1098Asp missense_variant Exon 25 of 26 ENST00000447648.7 NP_056210.1 Q7Z6L1-1
TECPR1XM_005250253.5 linkc.3293G>A p.Gly1098Asp missense_variant Exon 25 of 26 XP_005250310.1 Q7Z6L1-1
TECPR1XM_017011937.2 linkc.3191G>A p.Gly1064Asp missense_variant Exon 24 of 25 XP_016867426.1
TECPR1XM_047420119.1 linkc.3191G>A p.Gly1064Asp missense_variant Exon 24 of 25 XP_047276075.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TECPR1ENST00000447648.7 linkc.3293G>A p.Gly1098Asp missense_variant Exon 25 of 26 1 NM_015395.3 ENSP00000404923.2 Q7Z6L1-1

Frequencies

GnomAD3 genomes
AF:
0.0000920
AC:
14
AN:
152220
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000338
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000390
AC:
6
AN:
153892
Hom.:
0
AF XY:
0.0000367
AC XY:
3
AN XY:
81842
show subpopulations
Gnomad AFR exome
AF:
0.000636
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000168
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000786
AC:
11
AN:
1398608
Hom.:
0
Cov.:
34
AF XY:
0.00000725
AC XY:
5
AN XY:
689826
show subpopulations
Gnomad4 AFR exome
AF:
0.000158
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000280
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000463
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000853
AC:
13
AN:
152338
Hom.:
0
Cov.:
33
AF XY:
0.000121
AC XY:
9
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.000313
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000329
Hom.:
0
Bravo
AF:
0.0000718
ExAC
AF:
0.0000216
AC:
2

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Feb 03, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.3293G>A (p.G1098D) alteration is located in exon 25 (coding exon 23) of the TECPR1 gene. This alteration results from a G to A substitution at nucleotide position 3293, causing the glycine (G) at amino acid position 1098 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.50
BayesDel_addAF
Pathogenic
0.17
D
BayesDel_noAF
Uncertain
0.0
CADD
Pathogenic
27
DANN
Uncertain
1.0
DEOGEN2
Benign
0.27
T
Eigen
Uncertain
0.68
Eigen_PC
Uncertain
0.62
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.92
D
M_CAP
Benign
0.079
D
MetaRNN
Uncertain
0.64
D
MetaSVM
Benign
-0.71
T
MutationAssessor
Uncertain
2.5
M
PrimateAI
Uncertain
0.62
T
PROVEAN
Uncertain
-3.1
D
REVEL
Uncertain
0.41
Sift
Uncertain
0.0020
D
Sift4G
Uncertain
0.010
D
Polyphen
1.0
D
Vest4
0.96
MVP
0.62
MPC
0.99
ClinPred
0.61
D
GERP RS
4.3
Varity_R
0.64
gMVP
0.74

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs560814295; hg19: chr7-97847095; API