rs1553648931

Variant names:

• chr2-240874542-CCTGGCAACTGGAGGTGCCGTTCCCCAGAACAGAGAGGACTTCGGGGAGAAGTCAGGAATTCGGTGTTGGACGTGGGAGGTCTGAGATGCCAGCTGGACCACACGGGAGGGTGAAGGAAGCGGCTGGGTGTGAGTCAGGAGCCTGGGGAGAGGCCGGGGCTGGCCCCTCCATCTGGAGTTGTAGAGACGGACACATTTAAAGTTTCAAGCCTGGCCAGTGTCCCCTGGGGCCCGAAAGCAGTCACCTTTGGGTGATGTGAGAAATGAAGGCTGACCCTGTAGGAGGGGCTGGGGGAGAGAAAGGGGCACACAGAGTGGAGGGAGCTGGCCTTGGTGCCCCCATGGCAGGGTCACACAGCTGGGCCCAAGGGCCAGCGGGACTGGACAGCTGAGGGACCCACGACCCACCCGGTCCCACTCTGGCCCCTGAGCACAAATGCAGCTGGGGCGGGCCCTCCTGGGGGCCCCACCCCGTCTCACTCCCGTGAAACAGGACAGCCAGCGAGACTGCCCTGGCCTTCAGCCCAAACTGAGAGGCTGGTGCTCAGCCTGCTTCTTTCTCCCCAGAAAGAAGATGTACTCCCGCAAGACGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCTGGGGCTGTGACGACCAGCCCAGGATGTGAGGCCTGGCAGGGATGGGAAGGTGGAGGGCGCTGGGCATGGCTGAGAGGTGGGGCGCTGGCCTCTC-TGAGA
• rs1553648931
• NM_000030.3:c.680+480_776+69delCCTGGCAACTGGAGGTGCCGTTCCCCAGAACAGAGAGGACTTCGGGGAGAAGTCAGGAATTCGGTGTTGGACGTGGGAGGTCTGAGATGCCAGCTGGACCACACGGGAGGGTGAAGGAAGCGGCTGGGTGTGAGTCAGGAGCCTGGGGAGAGGCCGGGGCTGGCCCCTCCATCTGGAGTTGTAGAGACGGACACATTTAAAGTTTCAAGCCTGGCCAGTGTCCCCTGGGGCCCGAAAGCAGTCACCTTTGGGTGATGTGAGAAATGAAGGCTGACCCTGTAGGAGGGGCTGGGGGAGAGAAAGGGGCACACAGAGTGGAGGGAGCTGGCCTTGGTGCCCCCATGGCAGGGTCACACAGCTGGGCCCAAGGGCCAGCGGGACTGGACAGCTGAGGGACCCACGACCCACCCGGTCCCACTCTGGCCCCTGAGCACAAATGCAGCTGGGGCGGGCCCTCCTGGGGGCCCCACCCCGTCTCACTCCCGTGAAACAGGACAGCCAGCGAGACTGCCCTGGCCTTCAGCCCAAACTGAGAGGCTGGTGCTCAGCCTGCTTCTTTCTCCCCAGAAAGAAGATGTACTCCCGCAAGACGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCTGGGGCTGTGACGACCAGCCCAGGATGTGAGGCCTGGCAGGGATGGGAAGGTGGAGGGCGCTGGGCATGGCTGAGAGGTGGGGCGCTGGCCTCTCinsTGAGA

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1 PP5_Moderate

The NM_000030.3(AGXT):​c.680+480_776+69delCCTGGCAACTGGAGGTGCCGTTCCCCAGAACAGAGAGGACTTCGGGGAGAAGTCAGGAATTCGGTGTTGGACGTGGGAGGTCTGAGATGCCAGCTGGACCACACGGGAGGGTGAAGGAAGCGGCTGGGTGTGAGTCAGGAGCCTGGGGAGAGGCCGGGGCTGGCCCCTCCATCTGGAGTTGTAGAGACGGACACATTTAAAGTTTCAAGCCTGGCCAGTGTCCCCTGGGGCCCGAAAGCAGTCACCTTTGGGTGATGTGAGAAATGAAGGCTGACCCTGTAGGAGGGGCTGGGGGAGAGAAAGGGGCACACAGAGTGGAGGGAGCTGGCCTTGGTGCCCCCATGGCAGGGTCACACAGCTGGGCCCAAGGGCCAGCGGGACTGGACAGCTGAGGGACCCACGACCCACCCGGTCCCACTCTGGCCCCTGAGCACAAATGCAGCTGGGGCGGGCCCTCCTGGGGGCCCCACCCCGTCTCACTCCCGTGAAACAGGACAGCCAGCGAGACTGCCCTGGCCTTCAGCCCAAACTGAGAGGCTGGTGCTCAGCCTGCTTCTTTCTCCCCAGAAAGAAGATGTACTCCCGCAAGACGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCTGGGGCTGTGACGACCAGCCCAGGATGTGAGGCCTGGCAGGGATGGGAAGGTGGAGGGCGCTGGGCATGGCTGAGAGGTGGGGCGCTGGCCTCTCinsTGAGA​(p.Lys228_Met259del) variant causes a exon loss, splice acceptor, splice donor, splice region, synonymous, intron 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 DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 34)
• Consequence: AGXT NM_000030.3 exon_loss, splice_acceptor, splice_donor, splice_region, synonymous, intron
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 0.997
• Publications: 0 publications found

Genes affected

AGXT (HGNC:341): (alanine--glyoxylate aminotransferase) This gene is expressed only in the liver and the encoded protein is localized mostly in the peroxisomes, where it is involved in glyoxylate detoxification. Mutations in this gene, some of which alter subcellular targetting, have been associated with type I primary hyperoxaluria. [provided by RefSeq, Jul 2008]

AGXT Gene-Disease associations (from GenCC):

• alanine glyoxylate aminotransferase deficiency

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• primary hyperoxaluria type 1

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Myriad Women’s Health, Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PP5: Variant 2-240874542-CCTGGCAACTGGAGGTGCCGTTCCCCAGAACAGAGAGGACTTCGGGGAGAAGTCAGGAATTCGGTGTTGGACGTGGGAGGTCTGAGATGCCAGCTGGACCACACGGGAGGGTGAAGGAAGCGGCTGGGTGTGAGTCAGGAGCCTGGGGAGAGGCCGGGGCTGGCCCCTCCATCTGGAGTTGTAGAGACGGACACATTTAAAGTTTCAAGCCTGGCCAGTGTCCCCTGGGGCCCGAAAGCAGTCACCTTTGGGTGATGTGAGAAATGAAGGCTGACCCTGTAGGAGGGGCTGGGGGAGAGAAAGGGGCACACAGAGTGGAGGGAGCTGGCCTTGGTGCCCCCATGGCAGGGTCACACAGCTGGGCCCAAGGGCCAGCGGGACTGGACAGCTGAGGGACCCACGACCCACCCGGTCCCACTCTGGCCCCTGAGCACAAATGCAGCTGGGGCGGGCCCTCCTGGGGGCCCCACCCCGTCTCACTCCCGTGAAACAGGACAGCCAGCGAGACTGCCCTGGCCTTCAGCCCAAACTGAGAGGCTGGTGCTCAGCCTGCTTCTTTCTCCCCAGAAAGAAGATGTACTCCCGCAAGACGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCTGGGGCTGTGACGACCAGCCCAGGATGTGAGGCCTGGCAGGGATGGGAAGGTGGAGGGCGCTGGGCATGGCTGAGAGGTGGGGCGCTGGCCTCTC-TGAGA is Pathogenic according to our data. Variant chr2-240874542-CCTGGCAACTGGAGGTGCCGTTCCCCAGAACAGAGAGGACTTCGGGGAGAAGTCAGGAATTCGGTGTTGGACGTGGGAGGTCTGAGATGCCAGCTGGACCACACGGGAGGGTGAAGGAAGCGGCTGGGTGTGAGTCAGGAGCCTGGGGAGAGGCCGGGGCTGGCCCCTCCATCTGGAGTTGTAGAGACGGACACATTTAAAGTTTCAAGCCTGGCCAGTGTCCCCTGGGGCCCGAAAGCAGTCACCTTTGGGTGATGTGAGAAATGAAGGCTGACCCTGTAGGAGGGGCTGGGGGAGAGAAAGGGGCACACAGAGTGGAGGGAGCTGGCCTTGGTGCCCCCATGGCAGGGTCACACAGCTGGGCCCAAGGGCCAGCGGGACTGGACAGCTGAGGGACCCACGACCCACCCGGTCCCACTCTGGCCCCTGAGCACAAATGCAGCTGGGGCGGGCCCTCCTGGGGGCCCCACCCCGTCTCACTCCCGTGAAACAGGACAGCCAGCGAGACTGCCCTGGCCTTCAGCCCAAACTGAGAGGCTGGTGCTCAGCCTGCTTCTTTCTCCCCAGAAAGAAGATGTACTCCCGCAAGACGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCTGGGGCTGTGACGACCAGCCCAGGATGTGAGGCCTGGCAGGGATGGGAAGGTGGAGGGCGCTGGGCATGGCTGAGAGGTGGGGCGCTGGCCTCTC-TGAGA is described in ClinVar as Pathogenic. ClinVar VariationId is 204196.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000030.3. 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
	AGXT	NM_000030.3	MANE Select	c.680+480_776+69delCCTGGCAACTGGAGGTGCCGTTCCCCAGAACAGAGAGGACTTCGGGGAGAAGTCAGGAATTCGGTGTTGGACGTGGGAGGTCTGAGATGCCAGCTGGACCACACGGGAGGGTGAAGGAAGCGGCTGGGTGTGAGTCAGGAGCCTGGGGAGAGGCCGGGGCTGGCCCCTCCATCTGGAGTTGTAGAGACGGACACATTTAAAGTTTCAAGCCTGGCCAGTGTCCCCTGGGGCCCGAAAGCAGTCACCTTTGGGTGATGTGAGAAATGAAGGCTGACCCTGTAGGAGGGGCTGGGGGAGAGAAAGGGGCACACAGAGTGGAGGGAGCTGGCCTTGGTGCCCCCATGGCAGGGTCACACAGCTGGGCCCAAGGGCCAGCGGGACTGGACAGCTGAGGGACCCACGACCCACCCGGTCCCACTCTGGCCCCTGAGCACAAATGCAGCTGGGGCGGGCCCTCCTGGGGGCCCCACCCCGTCTCACTCCCGTGAAACAGGACAGCCAGCGAGACTGCCCTGGCCTTCAGCCCAAACTGAGAGGCTGGTGCTCAGCCTGCTTCTTTCTCCCCAGAAAGAAGATGTACTCCCGCAAGACGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCTGGGGCTGTGACGACCAGCCCAGGATGTGAGGCCTGGCAGGGATGGGAAGGTGGAGGGCGCTGGGCATGGCTGAGAGGTGGGGCGCTGGCCTCTCinsTGAGA	p.Lys228_Met259del	exon_loss splice_acceptor splice_donor splice_region synonymous intron	Exon 7 of 11	NP_000021.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGXT	ENST00000307503.4	TSL:1 MANE Select	c.680+480_776+69delCCTGGCAACTGGAGGTGCCGTTCCCCAGAACAGAGAGGACTTCGGGGAGAAGTCAGGAATTCGGTGTTGGACGTGGGAGGTCTGAGATGCCAGCTGGACCACACGGGAGGGTGAAGGAAGCGGCTGGGTGTGAGTCAGGAGCCTGGGGAGAGGCCGGGGCTGGCCCCTCCATCTGGAGTTGTAGAGACGGACACATTTAAAGTTTCAAGCCTGGCCAGTGTCCCCTGGGGCCCGAAAGCAGTCACCTTTGGGTGATGTGAGAAATGAAGGCTGACCCTGTAGGAGGGGCTGGGGGAGAGAAAGGGGCACACAGAGTGGAGGGAGCTGGCCTTGGTGCCCCCATGGCAGGGTCACACAGCTGGGCCCAAGGGCCAGCGGGACTGGACAGCTGAGGGACCCACGACCCACCCGGTCCCACTCTGGCCCCTGAGCACAAATGCAGCTGGGGCGGGCCCTCCTGGGGGCCCCACCCCGTCTCACTCCCGTGAAACAGGACAGCCAGCGAGACTGCCCTGGCCTTCAGCCCAAACTGAGAGGCTGGTGCTCAGCCTGCTTCTTTCTCCCCAGAAAGAAGATGTACTCCCGCAAGACGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCTGGGGCTGTGACGACCAGCCCAGGATGTGAGGCCTGGCAGGGATGGGAAGGTGGAGGGCGCTGGGCATGGCTGAGAGGTGGGGCGCTGGCCTCTCinsTGAGA	p.Lys228_Met259del	exon_loss splice_acceptor splice_donor splice_region synonymous intron	Exon 7 of 11	ENSP00000302620.3
	AGXT	ENST00000908247.1		c.687_857+69delCCTGGCAACTGGAGGTGCCGTTCCCCAGAACAGAGAGGACTTCGGGGAGAAGTCAGGAATTCGGTGTTGGACGTGGGAGGTCTGAGATGCCAGCTGGACCACACGGGAGGGTGAAGGAAGCGGCTGGGTGTGAGTCAGGAGCCTGGGGAGAGGCCGGGGCTGGCCCCTCCATCTGGAGTTGTAGAGACGGACACATTTAAAGTTTCAAGCCTGGCCAGTGTCCCCTGGGGCCCGAAAGCAGTCACCTTTGGGTGATGTGAGAAATGAAGGCTGACCCTGTAGGAGGGGCTGGGGGAGAGAAAGGGGCACACAGAGTGGAGGGAGCTGGCCTTGGTGCCCCCATGGCAGGGTCACACAGCTGGGCCCAAGGGCCAGCGGGACTGGACAGCTGAGGGACCCACGACCCACCCGGTCCCACTCTGGCCCCTGAGCACAAATGCAGCTGGGGCGGGCCCTCCTGGGGGCCCCACCCCGTCTCACTCCCGTGAAACAGGACAGCCAGCGAGACTGCCCTGGCCTTCAGCCCAAACTGAGAGGCTGGTGCTCAGCCTGCTTCTTTCTCCCCAGAAAGAAGATGTACTCCCGCAAGACGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCTGGGGCTGTGACGACCAGCCCAGGATGTGAGGCCTGGCAGGGATGGGAAGGTGGAGGGCGCTGGGCATGGCTGAGAGGTGGGGCGCTGGCCTCTCinsTGAGA	p.Ser229GlufsTer47	exon_loss frameshift missense	Exon 8 of 12	ENSP00000578306.1
	AGXT	ENST00000908232.1		c.681-28_827+69delCCTGGCAACTGGAGGTGCCGTTCCCCAGAACAGAGAGGACTTCGGGGAGAAGTCAGGAATTCGGTGTTGGACGTGGGAGGTCTGAGATGCCAGCTGGACCACACGGGAGGGTGAAGGAAGCGGCTGGGTGTGAGTCAGGAGCCTGGGGAGAGGCCGGGGCTGGCCCCTCCATCTGGAGTTGTAGAGACGGACACATTTAAAGTTTCAAGCCTGGCCAGTGTCCCCTGGGGCCCGAAAGCAGTCACCTTTGGGTGATGTGAGAAATGAAGGCTGACCCTGTAGGAGGGGCTGGGGGAGAGAAAGGGGCACACAGAGTGGAGGGAGCTGGCCTTGGTGCCCCCATGGCAGGGTCACACAGCTGGGCCCAAGGGCCAGCGGGACTGGACAGCTGAGGGACCCACGACCCACCCGGTCCCACTCTGGCCCCTGAGCACAAATGCAGCTGGGGCGGGCCCTCCTGGGGGCCCCACCCCGTCTCACTCCCGTGAAACAGGACAGCCAGCGAGACTGCCCTGGCCTTCAGCCCAAACTGAGAGGCTGGTGCTCAGCCTGCTTCTTTCTCCCCAGAAAGAAGATGTACTCCCGCAAGACGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCTGGGGCTGTGACGACCAGCCCAGGATGTGAGGCCTGGCAGGGATGGGAAGGTGGAGGGCGCTGGGCATGGCTGAGAGGTGGGGCGCTGGCCTCTCinsTGAGA	p.Thr228_Met276del	exon_loss synonymous	Exon 7 of 12	ENSP00000578291.1

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

ClinVar submissions as Germline

Significance: Pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
2	-	-	Primary hyperoxaluria, type I (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1553648931; hg19: chr2-241813959;