7-873320-CCT-AGA

Variant names:

• chr7-873320-CCT-AGA
• NM_001130965.3:c.2347_2349delCCTinsAGA
• SUN1 p.Pro783Arg

Variant summary

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

The NM_001130965.3(SUN1):​c.2347_2349delCCTinsAGA​(p.Pro783Arg) 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. P783H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 34)
• Consequence: SUN1 NM_001130965.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.96
• Publications: 0 publications found

Genes affected

SUN1 (HGNC:18587): (Sad1 and UNC84 domain containing 1) This gene is a member of the unc-84 homolog family and encodes a nuclear envelope protein with an Unc84 (SUN) domain. The protein is involved in nuclear anchorage and migration. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2019]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130965.3. 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
	SUN1	NM_001130965.3	MANE Select	c.2347_2349delCCTinsAGA	p.Pro783Arg	missense	N/A	NP_001124437.1	O94901-8
	SUN1	NM_001367651.1		c.2761_2763delCCTinsAGA	p.Pro921Arg	missense	N/A	NP_001354580.1
	SUN1	NM_001367705.1		c.2740_2742delCCTinsAGA	p.Pro914Arg	missense	N/A	NP_001354634.1	O94901-9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUN1	ENST00000401592.6	TSL:1 MANE Select	c.2347_2349delCCTinsAGA	p.Pro783Arg	missense	N/A	ENSP00000384015.1	O94901-8
	SUN1	ENST00000429178.5	TSL:1	c.2122_2124delCCTinsAGA	p.Pro708Arg	missense	N/A	ENSP00000409909.1	H0Y742
	SUN1	ENST00000475971.5	TSL:1	n.2456_2458delCCTinsAGA		non_coding_transcript_exon	Exon 10 of 10

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		6.0

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: chr7-912957;