NM_178554.6:c.51_52insTATCGACATGTGCTGTATCTATCGACAT

Variant names:

• chr3-134650909-C-CATGTCGATAGATACAGCACATGTCGATA
• rs1085307110
• NM_178554.6:c.51_52insTATCGACATGTGCTGTATCTATCGACAT

Variant summary

Our verdict is Uncertain significance. The variant received 5 ACMG points: 5P and 0B. PVS1_Strong PP5

The NM_178554.6(KY):​c.51_52insTATCGACATGTGCTGTATCTATCGACAT​(p.Val18TyrfsTer56) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. 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 INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: KY NM_178554.6 frameshift
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 0.257
• Publications: 1 publications found

Genes affected

KY (HGNC:26576): (kyphoscoliosis peptidase) The protein encoded by this gene belongs to the transglutaminase-like superfamily. The protein is involved in the function, maturation and stabilization of the neuromuscular junction and may be required for normal muscle growth. Mutations in this gene are associated with myopathy, myofibrillar, 7. [provided by RefSeq, Apr 2017]

ENSG00000288700 (HGNC:):

CEP63 (HGNC:25815): (centrosomal protein 63) This gene encodes a protein with six coiled-coil domains. The protein is localized to the centrosome, a non-membraneous organelle that functions as the major microtubule-organizing center in animal cells. Several alternatively spliced transcript variants have been found, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

CEP63 Gene-Disease associations (from GenCC):

• Seckel syndrome 6

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
• autosomal recessive primary microcephaly

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 5 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 8 pathogenic variants in the truncated region.
• PP5: Variant 3-134650909-C-CATGTCGATAGATACAGCACATGTCGATA is Pathogenic according to our data. Variant chr3-134650909-C-CATGTCGATAGATACAGCACATGTCGATA is described in ClinVar as Pathogenic. ClinVar VariationId is 402246.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178554.6. 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
	KY	NM_178554.6	MANE Select	c.51_52insTATCGACATGTGCTGTATCTATCGACAT	p.Val18TyrfsTer56	frameshift	Exon 1 of 11	NP_848649.3
	KY	NM_001350859.2		c.51_52insTATCGACATGTGCTGTATCTATCGACAT	p.Val18TyrfsTer56	frameshift	Exon 1 of 10	NP_001337788.1
	KY	NM_001366276.1		c.51_52insTATCGACATGTGCTGTATCTATCGACAT	p.Val18TyrfsTer56	frameshift	Exon 1 of 10	NP_001353205.1	Q8NBH2-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KY	ENST00000423778.7	TSL:5 MANE Select	c.51_52insTATCGACATGTGCTGTATCTATCGACAT	p.Val18TyrfsTer56	frameshift	Exon 1 of 11	ENSP00000397598.2	Q8NBH2-4
	KY	ENST00000503669.1	TSL:1	c.51_52insTATCGACATGTGCTGTATCTATCGACAT	p.Val18TyrfsTer56	frameshift	Exon 1 of 10	ENSP00000426777.1	B4DGA7
	KY	ENST00000864999.1		c.51_52insTATCGACATGTGCTGTATCTATCGACAT	p.Val18TyrfsTer38	frameshift	Exon 1 of 11	ENSP00000535058.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
1	-	-	Hereditary spastic paraplegia (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.26
Mutation Taster		=5/195	disease causing (ClinVar)

Splicing

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

Other links and lift over

dbSNP: rs1085307110; hg19: chr3-134369751;