20-4699373-T-TCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAG

Variant names:

• chr20-4699373-T-TCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAG
• rs367543047
• NM_000311.5:c.178_179insAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGC

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM4

The NM_000311.5(PRNP):​c.178_179insAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGC​(p.Gln59_Pro60insGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGln) variant causes a disruptive inframe insertion 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P60P) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PRNP NM_000311.5 disruptive_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.31
• Publications: 0 publications found

Genes affected

PRNP (HGNC:9449): (prion protein (Kanno blood group)) The protein encoded by this gene is a membrane glycosylphosphatidylinositol-anchored glycoprotein that tends to aggregate into rod-like structures. The encoded protein contains a highly unstable region of five tandem octapeptide repeats. This gene is found on chromosome 20, approximately 20 kbp upstream of a gene which encodes a biochemically and structurally similar protein to the one encoded by this gene. Mutations in the repeat region as well as elsewhere in this gene have been associated with Creutzfeldt-Jakob disease, fatal familial insomnia, Gerstmann-Straussler disease, Huntington disease-like 1, and kuru. An overlapping open reading frame has been found for this gene that encodes a smaller, structurally unrelated protein, AltPrp. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]

PRNP Gene-Disease associations (from GenCC):

• Gerstmann-Straussler-Scheinker syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Genomics England PanelApp, Orphanet
• Huntington disease-like 1

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet
• inherited Creutzfeldt-Jakob disease

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• familial Alzheimer-like prion disease

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• fatal familial insomnia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• PrP systemic amyloidosis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_000311.5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRNP	NM_000311.5	c.178_179insAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGC	p.Gln59_Pro60insGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGln	disruptive_inframe_insertion	Exon 2 of 2	ENST00000379440.9	NP_000302.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRNP	ENST00000379440.9	c.178_179insAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGC	p.Gln59_Pro60insGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGln	disruptive_inframe_insertion	Exon 2 of 2	1	NM_000311.5	ENSP00000368752.4
PRNP	ENST00000424424.2	c.178_179insAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGC	p.Gln59_Pro60insGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGln	disruptive_inframe_insertion	Exon 2 of 2	1		ENSP00000411599.2
PRNP	ENST00000430350.2	c.178_179insAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGC	p.Gln59_Pro60insGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGln	disruptive_inframe_insertion	Exon 2 of 2	1		ENSP00000399376.2
PRNP	ENST00000457586.2	c.178_179insAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGCAGGGCGGTGGTGGCTGGGGGCAGC	p.Gln59_Pro60insGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGlnGlnGlyGlyGlyGlyTrpGlyGln	disruptive_inframe_insertion	Exon 2 of 2	1		ENSP00000415284.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.3

Splicing

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

Other links and lift over

dbSNP: rs367543047; hg19: chr20-4680019;