chr7-98217710-GCC-TCG

Variant names:

• chr7-98217710-GCC-TCG
• NM_015395.3:c.3364_3366delGGCinsCGA
• TECPR1 p.Gly1122Arg

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_015395.3(TECPR1):​c.3364_3366delGGCinsCGA​(p.Gly1122Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1122V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 34)
• Consequence: TECPR1 NM_015395.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.90
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015395.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TECPR1	NM_015395.3	MANE Select	c.3364_3366delGGCinsCGA	p.Gly1122Arg	missense	N/A	NP_056210.1	Q7Z6L1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TECPR1	ENST00000447648.7	TSL:1 MANE Select	c.3364_3366delGGCinsCGA	p.Gly1122Arg	missense	N/A	ENSP00000404923.2	Q7Z6L1-1
	TECPR1	ENST00000490842.5	TSL:1	n.2562_2564delGGCinsCGA		non_coding_transcript_exon	Exon 14 of 16
	TECPR1	ENST00000871695.1		c.3364_3366delGGCinsCGA	p.Gly1122Arg	missense	N/A	ENSP00000541754.1

Frequencies

GnomAD3 genomes Cov.: 34

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr7-97847022;