5-140113537-CGCATGAGAGGGGGTGGCCGTGACTCGGTGTCCCCTCTTTGCAGGGGGCTCTGCTGCGCCGCGCAGGCCCCTCCTCCTACATCCTCTTTGGGGGGTCACTGGAAAGCAGAGCTTAGGCCCACTCTCTGTGCTTAGTATGGCAGACTCCTTCTCACCCCTAGTCCCCTAACTCCCCAGGCCGAGGCCGCCTAGGGTCTGCCCAACAGCGACAGCCACGGTGGTGGTGGTGGTGGTGGTGGTGGTAGCAGTGGTGGCGGCAGCAGCGGCAGCAGCAGCTGCGACGCTGCGCGTCCTGCTCCCTCTCCCCCACCCAGCCAGGGTTGTAGGGTGAGGGCCGGTGGGTGGGCGCCGCCTGGCGGGCGGGCGGACGGGGGGCTGGCAGCGGGGAGGGGGCGCAGGTCACGTGCCGGCGGGCGGGTGGGCGCGTACAGTAGGGCGCCCTGCTACTGTACTGGGGAGTCAGTGCCCTGTTACCGGGTCTCGTCTGTCTCGTCTCTCCCGCAGATCTCGCGAGAGTGGCTGACTGGCTGTGGGGGTTGCGGCGGCAGCAGGCGGAGCCGGGGAGGGAAAGCAGCGGCGGCTGAGGCGACTGAGGCGGCGGGCGGAGCGGCAGGCGGCGGCGGCGCGGCAGCGGAGCGCAGCATCATGGCGGACCGAGACAGCGGCAGCGAGCAGGGTGGTGCGGCGCTGGGTTCGGGCGGCTCCCTGGGGCACCCCGGCTCGGGCTCAGGCTCCGGCGGGGGCGGTGGTGGCGGCGGGGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGGGCCCCAGGGGGGCTGCAGCACGAGACGCAGGAGCTGGCCTCCAAGCGGGTGGACATCCAGAACAAGCGCTTCTACCTGGACGTGAAGCAGAACGCCAAGGGCCGCTTCCTGAAGAT-GAGGTGGG

Position:

chr5-140113537-CGCATGAGAGGGGGTGGCCGTGACTCGGTGTCCCCTCTTTGCAGGGGGCTCTGCTGCGCCGCGCAGGCCCCTCCTCCTACATCCTCTTTGGGGGGTCACTGGAAAGCAGAGCTTAGGCCCACTCTCTGTGCTTAGTATGGCAGACTCCTTCTCACCCCTAGTCCCCTAACTCCCCAGGCCGAGGCCGCCTAGGGTCTGCCCAACAGCGACAGCCACGGTGGTGGTGGTGGTGGTGGTGGTGGTAGCAGTGGTGGCGGCAGCAGCGGCAGCAGCAGCTGCGACGCTGCGCGTCCTGCTCCCTCTCCCCCACCCAGCCAGGGTTGTAGGGTGAGGGCCGGTGGGTGGGCGCCGCCTGGCGGGCGGGCGGACGGGGGGCTGGCAGCGGGGAGGGGGCGCAGGTCACGTGCCGGCGGGCGGGTGGGCGCGTACAGTAGGGCGCCCTGCTACTGTACTGGGGAGTCAGTGCCCTGTTACCGGGTCTCGTCTGTCTCGTCTCTCCCGCAGATCTCGCGAGAGTGGCTGACTGGCTGTGGGGGTTGCGGCGGCAGCAGGCGGAGCCGGGGAGGGAAAGCAGCGGCGGCTGAGGCGACTGAGGCGGCGGGCGGAGCGGCAGGCGGCGGCGGCGCGGCAGCGGAGCGCAGCATCATGGCGGACCGAGACAGCGGCAGCGAGCAGGGTGGTGCGGCGCTGGGTTCGGGCGGCTCCCTGGGGCACCCCGGCTCGGGCTCAGGCTCCGGCGGGGGCGGTGGTGGCGGCGGGGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGGGCCCCAGGGGGGCTGCAGCACGAGACGCAGGAGCTGGCCTCCAAGCGGGTGGACATCCAGAACAAGCGCTTCTACCTGGACGTGAAGCAGAACGCCAAGGGCCGCTTCCTGAAGAT-GAGGTGGG

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate

The NM_005859.5(PURA):c.-645_263delCGCATGAGAGGGGGTGGCCGTGACTCGGTGTCCCCTCTTTGCAGGGGGCTCTGCTGCGCCGCGCAGGCCCCTCCTCCTACATCCTCTTTGGGGGGTCACTGGAAAGCAGAGCTTAGGCCCACTCTCTGTGCTTAGTATGGCAGACTCCTTCTCACCCCTAGTCCCCTAACTCCCCAGGCCGAGGCCGCCTAGGGTCTGCCCAACAGCGACAGCCACGGTGGTGGTGGTGGTGGTGGTGGTGGTAGCAGTGGTGGCGGCAGCAGCGGCAGCAGCAGCTGCGACGCTGCGCGTCCTGCTCCCTCTCCCCCACCCAGCCAGGGTTGTAGGGTGAGGGCCGGTGGGTGGGCGCCGCCTGGCGGGCGGGCGGACGGGGGGCTGGCAGCGGGGAGGGGGCGCAGGTCACGTGCCGGCGGGCGGGTGGGCGCGTACAGTAGGGCGCCCTGCTACTGTACTGGGGAGTCAGTGCCCTGTTACCGGGTCTCGTCTGTCTCGTCTCTCCCGCAGATCTCGCGAGAGTGGCTGACTGGCTGTGGGGGTTGCGGCGGCAGCAGGCGGAGCCGGGGAGGGAAAGCAGCGGCGGCTGAGGCGACTGAGGCGGCGGGCGGAGCGGCAGGCGGCGGCGGCGCGGCAGCGGAGCGCAGCATCATGGCGGACCGAGACAGCGGCAGCGAGCAGGGTGGTGCGGCGCTGGGTTCGGGCGGCTCCCTGGGGCACCCCGGCTCGGGCTCAGGCTCCGGCGGGGGCGGTGGTGGCGGCGGGGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGGGCCCCAGGGGGGCTGCAGCACGAGACGCAGGAGCTGGCCTCCAAGCGGGTGGACATCCAGAACAAGCGCTTCTACCTGGACGTGAAGCAGAACGCCAAGGGCCGCTTCCTGAAGATinsGAGGTGGG(p.Met1_Ile88delins???) variant causes a start lost, conservative inframe deletion, synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

Frequency

Genomes: not found (cov: 32)

Consequence

PURA
NM_005859.5 start_lost, conservative_inframe_deletion, synonymous

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 2.55

Variant links:

Genes affected

PURA (HGNC:9701): (purine rich element binding protein A) This gene product is a sequence-specific, single-stranded DNA-binding protein. It binds preferentially to the single strand of the purine-rich element termed PUR, which is present at origins of replication and in gene flanking regions in a variety of eukaryotes from yeasts through humans. Thus, it is implicated in the control of both DNA replication and transcription. Deletion of this gene has been associated with myelodysplastic syndrome and acute myelogenous leukemia. [provided by RefSeq, Jul 2008]

PURA links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PVS1

Start lost variant, no new inframe start found.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 5-140113537-CGCATGAGAGGGGGTGGCCGTGACTCGGTGTCCCCTCTTTGCAGGGGGCTCTGCTGCGCCGCGCAGGCCCCTCCTCCTACATCCTCTTTGGGGGGTCACTGGAAAGCAGAGCTTAGGCCCACTCTCTGTGCTTAGTATGGCAGACTCCTTCTCACCCCTAGTCCCCTAACTCCCCAGGCCGAGGCCGCCTAGGGTCTGCCCAACAGCGACAGCCACGGTGGTGGTGGTGGTGGTGGTGGTGGTAGCAGTGGTGGCGGCAGCAGCGGCAGCAGCAGCTGCGACGCTGCGCGTCCTGCTCCCTCTCCCCCACCCAGCCAGGGTTGTAGGGTGAGGGCCGGTGGGTGGGCGCCGCCTGGCGGGCGGGCGGACGGGGGGCTGGCAGCGGGGAGGGGGCGCAGGTCACGTGCCGGCGGGCGGGTGGGCGCGTACAGTAGGGCGCCCTGCTACTGTACTGGGGAGTCAGTGCCCTGTTACCGGGTCTCGTCTGTCTCGTCTCTCCCGCAGATCTCGCGAGAGTGGCTGACTGGCTGTGGGGGTTGCGGCGGCAGCAGGCGGAGCCGGGGAGGGAAAGCAGCGGCGGCTGAGGCGACTGAGGCGGCGGGCGGAGCGGCAGGCGGCGGCGGCGCGGCAGCGGAGCGCAGCATCATGGCGGACCGAGACAGCGGCAGCGAGCAGGGTGGTGCGGCGCTGGGTTCGGGCGGCTCCCTGGGGCACCCCGGCTCGGGCTCAGGCTCCGGCGGGGGCGGTGGTGGCGGCGGGGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGGGCCCCAGGGGGGCTGCAGCACGAGACGCAGGAGCTGGCCTCCAAGCGGGTGGACATCCAGAACAAGCGCTTCTACCTGGACGTGAAGCAGAACGCCAAGGGCCGCTTCCTGAAGAT-GAGGTGGG is Pathogenic according to our data. Variant chr5-140113537-CGCATGAGAGGGGGTGGCCGTGACTCGGTGTCCCCTCTTTGCAGGGGGCTCTGCTGCGCCGCGCAGGCCCCTCCTCCTACATCCTCTTTGGGGGGTCACTGGAAAGCAGAGCTTAGGCCCACTCTCTGTGCTTAGTATGGCAGACTCCTTCTCACCCCTAGTCCCCTAACTCCCCAGGCCGAGGCCGCCTAGGGTCTGCCCAACAGCGACAGCCACGGTGGTGGTGGTGGTGGTGGTGGTGGTAGCAGTGGTGGCGGCAGCAGCGGCAGCAGCAGCTGCGACGCTGCGCGTCCTGCTCCCTCTCCCCCACCCAGCCAGGGTTGTAGGGTGAGGGCCGGTGGGTGGGCGCCGCCTGGCGGGCGGGCGGACGGGGGGCTGGCAGCGGGGAGGGGGCGCAGGTCACGTGCCGGCGGGCGGGTGGGCGCGTACAGTAGGGCGCCCTGCTACTGTACTGGGGAGTCAGTGCCCTGTTACCGGGTCTCGTCTGTCTCGTCTCTCCCGCAGATCTCGCGAGAGTGGCTGACTGGCTGTGGGGGTTGCGGCGGCAGCAGGCGGAGCCGGGGAGGGAAAGCAGCGGCGGCTGAGGCGACTGAGGCGGCGGGCGGAGCGGCAGGCGGCGGCGGCGCGGCAGCGGAGCGCAGCATCATGGCGGACCGAGACAGCGGCAGCGAGCAGGGTGGTGCGGCGCTGGGTTCGGGCGGCTCCCTGGGGCACCCCGGCTCGGGCTCAGGCTCCGGCGGGGGCGGTGGTGGCGGCGGGGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGGGCCCCAGGGGGGCTGCAGCACGAGACGCAGGAGCTGGCCTCCAAGCGGGTGGACATCCAGAACAAGCGCTTCTACCTGGACGTGAAGCAGAACGCCAAGGGCCGCTTCCTGAAGAT-GAGGTGGG is described in ClinVar as [Pathogenic]. Clinvar id is 2861228.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PURA	NM_005859.5 link	c.-645_263delCGCATGAGAGGGGGTGGCCGTGACTCGGTGTCCCCTCTTTGCAGGGGGCTCTGCTGCGCCGCGCAGGCCCCTCCTCCTACATCCTCTTTGGGGGGTCACTGGAAAGCAGAGCTTAGGCCCACTCTCTGTGCTTAGTATGGCAGACTCCTTCTCACCCCTAGTCCCCTAACTCCCCAGGCCGAGGCCGCCTAGGGTCTGCCCAACAGCGACAGCCACGGTGGTGGTGGTGGTGGTGGTGGTGGTAGCAGTGGTGGCGGCAGCAGCGGCAGCAGCAGCTGCGACGCTGCGCGTCCTGCTCCCTCTCCCCCACCCAGCCAGGGTTGTAGGGTGAGGGCCGGTGGGTGGGCGCCGCCTGGCGGGCGGGCGGACGGGGGGCTGGCAGCGGGGAGGGGGCGCAGGTCACGTGCCGGCGGGCGGGTGGGCGCGTACAGTAGGGCGCCCTGCTACTGTACTGGGGAGTCAGTGCCCTGTTACCGGGTCTCGTCTGTCTCGTCTCTCCCGCAGATCTCGCGAGAGTGGCTGACTGGCTGTGGGGGTTGCGGCGGCAGCAGGCGGAGCCGGGGAGGGAAAGCAGCGGCGGCTGAGGCGACTGAGGCGGCGGGCGGAGCGGCAGGCGGCGGCGGCGCGGCAGCGGAGCGCAGCATCATGGCGGACCGAGACAGCGGCAGCGAGCAGGGTGGTGCGGCGCTGGGTTCGGGCGGCTCCCTGGGGCACCCCGGCTCGGGCTCAGGCTCCGGCGGGGGCGGTGGTGGCGGCGGGGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGGGCCCCAGGGGGGCTGCAGCACGAGACGCAGGAGCTGGCCTCCAAGCGGGTGGACATCCAGAACAAGCGCTTCTACCTGGACGTGAAGCAGAACGCCAAGGGCCGCTTCCTGAAGATinsGAGGTGGG	p.Met1_Ile88delins???	start_lost, conservative_inframe_deletion, synonymous_variant	1/1	ENST00000331327.5	NP_005850.1	Q00577
PURA	NM_005859.5 link	c.-645_263delCGCATGAGAGGGGGTGGCCGTGACTCGGTGTCCCCTCTTTGCAGGGGGCTCTGCTGCGCCGCGCAGGCCCCTCCTCCTACATCCTCTTTGGGGGGTCACTGGAAAGCAGAGCTTAGGCCCACTCTCTGTGCTTAGTATGGCAGACTCCTTCTCACCCCTAGTCCCCTAACTCCCCAGGCCGAGGCCGCCTAGGGTCTGCCCAACAGCGACAGCCACGGTGGTGGTGGTGGTGGTGGTGGTGGTAGCAGTGGTGGCGGCAGCAGCGGCAGCAGCAGCTGCGACGCTGCGCGTCCTGCTCCCTCTCCCCCACCCAGCCAGGGTTGTAGGGTGAGGGCCGGTGGGTGGGCGCCGCCTGGCGGGCGGGCGGACGGGGGGCTGGCAGCGGGGAGGGGGCGCAGGTCACGTGCCGGCGGGCGGGTGGGCGCGTACAGTAGGGCGCCCTGCTACTGTACTGGGGAGTCAGTGCCCTGTTACCGGGTCTCGTCTGTCTCGTCTCTCCCGCAGATCTCGCGAGAGTGGCTGACTGGCTGTGGGGGTTGCGGCGGCAGCAGGCGGAGCCGGGGAGGGAAAGCAGCGGCGGCTGAGGCGACTGAGGCGGCGGGCGGAGCGGCAGGCGGCGGCGGCGCGGCAGCGGAGCGCAGCATCATGGCGGACCGAGACAGCGGCAGCGAGCAGGGTGGTGCGGCGCTGGGTTCGGGCGGCTCCCTGGGGCACCCCGGCTCGGGCTCAGGCTCCGGCGGGGGCGGTGGTGGCGGCGGGGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGGGCCCCAGGGGGGCTGCAGCACGAGACGCAGGAGCTGGCCTCCAAGCGGGTGGACATCCAGAACAAGCGCTTCTACCTGGACGTGAAGCAGAACGCCAAGGGCCGCTTCCTGAAGATinsGAGGTGGG		5_prime_UTR_variant	1/1	ENST00000331327.5	NP_005850.1	Q00577
PURA	NM_005859.5 link	c.-645_263delCGCATGAGAGGGGGTGGCCGTGACTCGGTGTCCCCTCTTTGCAGGGGGCTCTGCTGCGCCGCGCAGGCCCCTCCTCCTACATCCTCTTTGGGGGGTCACTGGAAAGCAGAGCTTAGGCCCACTCTCTGTGCTTAGTATGGCAGACTCCTTCTCACCCCTAGTCCCCTAACTCCCCAGGCCGAGGCCGCCTAGGGTCTGCCCAACAGCGACAGCCACGGTGGTGGTGGTGGTGGTGGTGGTGGTAGCAGTGGTGGCGGCAGCAGCGGCAGCAGCAGCTGCGACGCTGCGCGTCCTGCTCCCTCTCCCCCACCCAGCCAGGGTTGTAGGGTGAGGGCCGGTGGGTGGGCGCCGCCTGGCGGGCGGGCGGACGGGGGGCTGGCAGCGGGGAGGGGGCGCAGGTCACGTGCCGGCGGGCGGGTGGGCGCGTACAGTAGGGCGCCCTGCTACTGTACTGGGGAGTCAGTGCCCTGTTACCGGGTCTCGTCTGTCTCGTCTCTCCCGCAGATCTCGCGAGAGTGGCTGACTGGCTGTGGGGGTTGCGGCGGCAGCAGGCGGAGCCGGGGAGGGAAAGCAGCGGCGGCTGAGGCGACTGAGGCGGCGGGCGGAGCGGCAGGCGGCGGCGGCGCGGCAGCGGAGCGCAGCATCATGGCGGACCGAGACAGCGGCAGCGAGCAGGGTGGTGCGGCGCTGGGTTCGGGCGGCTCCCTGGGGCACCCCGGCTCGGGCTCAGGCTCCGGCGGGGGCGGTGGTGGCGGCGGGGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGGGCCCCAGGGGGGCTGCAGCACGAGACGCAGGAGCTGGCCTCCAAGCGGGTGGACATCCAGAACAAGCGCTTCTACCTGGACGTGAAGCAGAACGCCAAGGGCCGCTTCCTGAAGATinsGAGGTGGG		upstream_gene_variant		ENST00000331327.5	NP_005850.1	Q00577

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PURA	ENST00000331327.5 link	c.-645_263delCGCATGAGAGGGGGTGGCCGTGACTCGGTGTCCCCTCTTTGCAGGGGGCTCTGCTGCGCCGCGCAGGCCCCTCCTCCTACATCCTCTTTGGGGGGTCACTGGAAAGCAGAGCTTAGGCCCACTCTCTGTGCTTAGTATGGCAGACTCCTTCTCACCCCTAGTCCCCTAACTCCCCAGGCCGAGGCCGCCTAGGGTCTGCCCAACAGCGACAGCCACGGTGGTGGTGGTGGTGGTGGTGGTGGTAGCAGTGGTGGCGGCAGCAGCGGCAGCAGCAGCTGCGACGCTGCGCGTCCTGCTCCCTCTCCCCCACCCAGCCAGGGTTGTAGGGTGAGGGCCGGTGGGTGGGCGCCGCCTGGCGGGCGGGCGGACGGGGGGCTGGCAGCGGGGAGGGGGCGCAGGTCACGTGCCGGCGGGCGGGTGGGCGCGTACAGTAGGGCGCCCTGCTACTGTACTGGGGAGTCAGTGCCCTGTTACCGGGTCTCGTCTGTCTCGTCTCTCCCGCAGATCTCGCGAGAGTGGCTGACTGGCTGTGGGGGTTGCGGCGGCAGCAGGCGGAGCCGGGGAGGGAAAGCAGCGGCGGCTGAGGCGACTGAGGCGGCGGGCGGAGCGGCAGGCGGCGGCGGCGCGGCAGCGGAGCGCAGCATCATGGCGGACCGAGACAGCGGCAGCGAGCAGGGTGGTGCGGCGCTGGGTTCGGGCGGCTCCCTGGGGCACCCCGGCTCGGGCTCAGGCTCCGGCGGGGGCGGTGGTGGCGGCGGGGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGGGCCCCAGGGGGGCTGCAGCACGAGACGCAGGAGCTGGCCTCCAAGCGGGTGGACATCCAGAACAAGCGCTTCTACCTGGACGTGAAGCAGAACGCCAAGGGCCGCTTCCTGAAGATinsGAGGTGGG	p.Met1_Ile88delins???	start_lost, conservative_inframe_deletion, synonymous_variant	1/1	6	NM_005859.5	ENSP00000332706.3	Q00577
PURA	ENST00000331327 link	c.-645_263delCGCATGAGAGGGGGTGGCCGTGACTCGGTGTCCCCTCTTTGCAGGGGGCTCTGCTGCGCCGCGCAGGCCCCTCCTCCTACATCCTCTTTGGGGGGTCACTGGAAAGCAGAGCTTAGGCCCACTCTCTGTGCTTAGTATGGCAGACTCCTTCTCACCCCTAGTCCCCTAACTCCCCAGGCCGAGGCCGCCTAGGGTCTGCCCAACAGCGACAGCCACGGTGGTGGTGGTGGTGGTGGTGGTGGTAGCAGTGGTGGCGGCAGCAGCGGCAGCAGCAGCTGCGACGCTGCGCGTCCTGCTCCCTCTCCCCCACCCAGCCAGGGTTGTAGGGTGAGGGCCGGTGGGTGGGCGCCGCCTGGCGGGCGGGCGGACGGGGGGCTGGCAGCGGGGAGGGGGCGCAGGTCACGTGCCGGCGGGCGGGTGGGCGCGTACAGTAGGGCGCCCTGCTACTGTACTGGGGAGTCAGTGCCCTGTTACCGGGTCTCGTCTGTCTCGTCTCTCCCGCAGATCTCGCGAGAGTGGCTGACTGGCTGTGGGGGTTGCGGCGGCAGCAGGCGGAGCCGGGGAGGGAAAGCAGCGGCGGCTGAGGCGACTGAGGCGGCGGGCGGAGCGGCAGGCGGCGGCGGCGCGGCAGCGGAGCGCAGCATCATGGCGGACCGAGACAGCGGCAGCGAGCAGGGTGGTGCGGCGCTGGGTTCGGGCGGCTCCCTGGGGCACCCCGGCTCGGGCTCAGGCTCCGGCGGGGGCGGTGGTGGCGGCGGGGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGGGCCCCAGGGGGGCTGCAGCACGAGACGCAGGAGCTGGCCTCCAAGCGGGTGGACATCCAGAACAAGCGCTTCTACCTGGACGTGAAGCAGAACGCCAAGGGCCGCTTCCTGAAGATinsGAGGTGGG		5_prime_UTR_variant	1/1		NM_005859.5	ENSP00000332706.3	Q00577
PURA	ENST00000331327.5 link	c.-645_263delCGCATGAGAGGGGGTGGCCGTGACTCGGTGTCCCCTCTTTGCAGGGGGCTCTGCTGCGCCGCGCAGGCCCCTCCTCCTACATCCTCTTTGGGGGGTCACTGGAAAGCAGAGCTTAGGCCCACTCTCTGTGCTTAGTATGGCAGACTCCTTCTCACCCCTAGTCCCCTAACTCCCCAGGCCGAGGCCGCCTAGGGTCTGCCCAACAGCGACAGCCACGGTGGTGGTGGTGGTGGTGGTGGTGGTAGCAGTGGTGGCGGCAGCAGCGGCAGCAGCAGCTGCGACGCTGCGCGTCCTGCTCCCTCTCCCCCACCCAGCCAGGGTTGTAGGGTGAGGGCCGGTGGGTGGGCGCCGCCTGGCGGGCGGGCGGACGGGGGGCTGGCAGCGGGGAGGGGGCGCAGGTCACGTGCCGGCGGGCGGGTGGGCGCGTACAGTAGGGCGCCCTGCTACTGTACTGGGGAGTCAGTGCCCTGTTACCGGGTCTCGTCTGTCTCGTCTCTCCCGCAGATCTCGCGAGAGTGGCTGACTGGCTGTGGGGGTTGCGGCGGCAGCAGGCGGAGCCGGGGAGGGAAAGCAGCGGCGGCTGAGGCGACTGAGGCGGCGGGCGGAGCGGCAGGCGGCGGCGGCGCGGCAGCGGAGCGCAGCATCATGGCGGACCGAGACAGCGGCAGCGAGCAGGGTGGTGCGGCGCTGGGTTCGGGCGGCTCCCTGGGGCACCCCGGCTCGGGCTCAGGCTCCGGCGGGGGCGGTGGTGGCGGCGGGGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGGGCCCCAGGGGGGCTGCAGCACGAGACGCAGGAGCTGGCCTCCAAGCGGGTGGACATCCAGAACAAGCGCTTCTACCTGGACGTGAAGCAGAACGCCAAGGGCCGCTTCCTGAAGATinsGAGGTGGG		upstream_gene_variant		6	NM_005859.5	ENSP00000332706.3	Q00577

Frequencies

GnomAD3 genomes

Cov.:

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Cov.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 04, 2023

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PURA-related conditions. This variant results in the deletion of part of exon 1 (c.-645_263delinsGAGGTGGG) of the PURA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PURA are known to be pathogenic (PMID: 29097605). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

No publications associated with this variant yet.