7-55939671-CTG-GTT

Variant names:

• chr7-55939671-CTG-GTT
• NM_182633.3:c.997_999delCTGinsGTT
• ZNF713 p.Leu333Val

Variant summary

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

The NM_182633.3(ZNF713):​c.997_999delCTGinsGTT​(p.Leu333Val) 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZNF713 NM_182633.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.68
• Publications: 0 publications found

Genes affected

ZNF713 (HGNC:22043): (zinc finger protein 713) The protein encoded by this gene contains C2H2 zinc finger domains. In some individuals, a CGG-repeat expansion from 5-22 repeats to 68-450 repeats has been identified in the first intron of this gene. This mutation is thought to effect the expression of this gene and it has been proposed that it may be associated with Autistic Spectrum Disorder. [provided by RefSeq, Jul 2016]

ZNF713 Gene-Disease associations (from GenCC):

• autism

  Inheritance: AD Classification: LIMITED Submitted by: G2P

ENSG00000249773 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182633.3. 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
	ZNF713	NM_182633.3	MANE Select	c.997_999delCTGinsGTT	p.Leu333Val	missense	N/A	NP_872439.2	Q8N859
	ZNF713	NM_001366796.2		c.958_960delCTGinsGTT	p.Leu320Val	missense	N/A	NP_001353725.1	A0A8I5JYA4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF713	ENST00000429591.4	TSL:5 MANE Select	c.997_999delCTGinsGTT	p.Leu333Val	missense	N/A	ENSP00000416662.3	Q8N859
	ZNF713	ENST00000633730.1	TSL:1	c.958_960delCTGinsGTT	p.Leu320Val	missense	N/A	ENSP00000487818.1	A0A8I5JYA4
	ENSG00000249773	ENST00000426595.1	TSL:5	c.269-13508_269-13506delCTGinsGTT		intron	N/A	ENSP00000390331.1	I3L0E3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.7

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: chr7-56007364;