rs397507441

Variant names:

• chr7-142750576-A-ATGACAAGAT
• rs397507441
• NM_002769.5:c.63_71dupTGACAAGAT

Variant summary

Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B. PM1 PM2 PM4

The NM_002769.5(PRSS1):​c.63_71dupTGACAAGAT​(p.Ile24_Val25insAspLysIle) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. I24I) has been classified as Benign.

• Frequency: Genomes: not found (cov: 40)
• Consequence: PRSS1 NM_002769.5 disruptive_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 4 publications found

Genes affected

PRSS1 (HGNC:9475): (serine protease 1) This gene encodes a trypsinogen, which is a member of the trypsin family of serine proteases. This enzyme is secreted by the pancreas and cleaved to its active form in the small intestine. It is active on peptide linkages involving the carboxyl group of lysine or arginine. Mutations in this gene are associated with hereditary pancreatitis. This gene and several other trypsinogen genes are localized to the T cell receptor beta locus on chromosome 7. [provided by RefSeq, Jul 2008]

PRSS1 Gene-Disease associations (from GenCC):

• hereditary chronic pancreatitis

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Illumina, Orphanet, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics, PanelApp Australia
• malignant pancreatic neoplasm

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp

TRB (HGNC:12155):

ACMG classification

Our verdict: Likely_pathogenic. The variant received 6 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 32 uncertain in NM_002769.5
• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_002769.5.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002769.5. 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
	PRSS1	NM_002769.5	MANE Select	c.63_71dupTGACAAGAT	p.Ile24_Val25insAspLysIle	disruptive_inframe_insertion	Exon 2 of 5	NP_002760.1
	PRSS1	NR_172947.1		n.76_84dupTGACAAGAT		non_coding_transcript_exon	Exon 2 of 5
	PRSS1	NR_172948.1		n.76_84dupTGACAAGAT		non_coding_transcript_exon	Exon 2 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRSS1	ENST00000311737.12	TSL:1 MANE Select	c.63_71dupTGACAAGAT	p.Ile24_Val25insAspLysIle	disruptive_inframe_insertion	Exon 2 of 5	ENSP00000308720.7
	PRSS1	ENST00000486171.5	TSL:5	c.63_71dupTGACAAGAT	p.Ile24_Val25insAspLysIle	disruptive_inframe_insertion	Exon 2 of 6	ENSP00000417854.1
	PRSS1	ENST00000492062.2	TSL:2	c.63_71dupTGACAAGAT	p.Ile24_Val25insAspLysIle	disruptive_inframe_insertion	Exon 2 of 5	ENSP00000419912.2

Frequencies

GnomAD3 genomes Cov.: 40

GnomAD4 exome Cov.: 98

GnomAD4 genome Cov.: 40

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.078
Mutation Taster		=54/46	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs397507441; hg19: chr7-142458427;