rs1555268712

Variant names:

• chr12-101757459-C-CATATAAATTTTAGAACAGTGCTTAATAGACAAAATATTGTAGAATTATAAAAAAGCCAGACCTTTGTGATTACTCTTATACTAAACAAAGGGAGTATGCGTGTACTACTTACCTATATTTGTTTTTGTCCTTATATGCTTTGTGGATTTTGTCAGTTACTGGTTTACAGTTTGTTACTAGACTTTTAGTGACCGGTGGCTATGAGAAA
• rs1555268712
• NM_024312.5:c.3250-10_3335+112dupTTTCTCATAGCCACCGGTCACTAAAAGTCTAGTAACAAACTGTAAACCAGTAACTGACAAAATCCACAAAGCATATAAGGACAAAAACAAATATAGGTAAGTAGTACACGCATACTCCCTTTGTTTAGTATAAGAGTAATCACAAAGGTCTGGCTTTTTTATAATTCTACAATATTTTGTCTATTAAGCACTGTTCTAAAATTTATAT

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP5_Moderate

The NM_024312.5(GNPTAB):​c.3250-10_3335+112dupTTTCTCATAGCCACCGGTCACTAAAAGTCTAGTAACAAACTGTAAACCAGTAACTGACAAAATCCACAAAGCATATAAGGACAAAAACAAATATAGGTAAGTAGTACACGCATACTCCCTTTGTTTAGTATAAGAGTAATCACAAAGGTCTGGCTTTTTTATAATTCTACAATATTTTGTCTATTAAGCACTGTTCTAAAATTTATAT variant causes a intron 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 Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: GNPTAB NM_024312.5 intron
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 0.354

Genes affected

GNPTAB (HGNC:29670): (N-acetylglucosamine-1-phosphate transferase subunits alpha and beta) This gene encodes two of three subunit types of the membrane-bound enzyme N-acetylglucosamine-1-phosphotransferase, a heterohexameric complex composed of two alpha, two beta, and two gamma subunits. The encoded protein is proteolytically cleaved at the Lys928-Asp929 bond to yield mature alpha and beta polypeptides while the gamma subunits are the product of a distinct gene (GeneID 84572). In the Golgi apparatus, the heterohexameric complex catalyzes the first step in the synthesis of mannose 6-phosphate recognition markers on certain oligosaccharides of newly synthesized lysosomal enzymes. These recognition markers are essential for appropriate trafficking of lysosomal enzymes. Mutations in this gene have been associated with both mucolipidosis II and mucolipidosis IIIA.[provided by RefSeq, May 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 12-101757459-C-CATATAAATTTTAGAACAGTGCTTAATAGACAAAATATTGTAGAATTATAAAAAAGCCAGACCTTTGTGATTACTCTTATACTAAACAAAGGGAGTATGCGTGTACTACTTACCTATATTTGTTTTTGTCCTTATATGCTTTGTGGATTTTGTCAGTTACTGGTTTACAGTTTGTTACTAGACTTTTAGTGACCGGTGGCTATGAGAAA is Pathogenic according to our data. Variant chr12-101757459-C-CATATAAATTTTAGAACAGTGCTTAATAGACAAAATATTGTAGAATTATAAAAAAGCCAGACCTTTGTGATTACTCTTATACTAAACAAAGGGAGTATGCGTGTACTACTTACCTATATTTGTTTTTGTCCTTATATGCTTTGTGGATTTTGTCAGTTACTGGTTTACAGTTTGTTACTAGACTTTTAGTGACCGGTGGCTATGAGAAA is described in ClinVar as [Likely_pathogenic]. Clinvar id is 397571.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNPTAB	NM_024312.5	c.3250-10_3335+112dupTTTCTCATAGCCACCGGTCACTAAAAGTCTAGTAACAAACTGTAAACCAGTAACTGACAAAATCCACAAAGCATATAAGGACAAAAACAAATATAGGTAAGTAGTACACGCATACTCCCTTTGTTTAGTATAAGAGTAATCACAAAGGTCTGGCTTTTTTATAATTCTACAATATTTTGTCTATTAAGCACTGTTCTAAAATTTATAT		intron_variant	Intron 17 of 20	ENST00000299314.12	NP_077288.2
GNPTAB	XM_011538731.3	c.3169-10_3254+112dupTTTCTCATAGCCACCGGTCACTAAAAGTCTAGTAACAAACTGTAAACCAGTAACTGACAAAATCCACAAAGCATATAAGGACAAAAACAAATATAGGTAAGTAGTACACGCATACTCCCTTTGTTTAGTATAAGAGTAATCACAAAGGTCTGGCTTTTTTATAATTCTACAATATTTTGTCTATTAAGCACTGTTCTAAAATTTATAT		intron_variant	Intron 17 of 20		XP_011537033.1
GNPTAB	XM_006719593.4	c.3250-10_3335+112dupTTTCTCATAGCCACCGGTCACTAAAAGTCTAGTAACAAACTGTAAACCAGTAACTGACAAAATCCACAAAGCATATAAGGACAAAAACAAATATAGGTAAGTAGTACACGCATACTCCCTTTGTTTAGTATAAGAGTAATCACAAAGGTCTGGCTTTTTTATAATTCTACAATATTTTGTCTATTAAGCACTGTTCTAAAATTTATAT		intron_variant	Intron 17 of 18		XP_006719656.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNPTAB	ENST00000299314.12	c.3335+112_3335+113insTTTCTCATAGCCACCGGTCACTAAAAGTCTAGTAACAAACTGTAAACCAGTAACTGACAAAATCCACAAAGCATATAAGGACAAAAACAAATATAGGTAAGTAGTACACGCATACTCCCTTTGTTTAGTATAAGAGTAATCACAAAGGTCTGGCTTTTTTATAATTCTACAATATTTTGTCTATTAAGCACTGTTCTAAAATTTATAT		intron_variant	Intron 17 of 20	1	NM_024312.5	ENSP00000299314.7
GNPTAB	ENST00000550718.1	c.146+112_146+113insTTTCTCATAGCCACCGGTCACTAAAAGTCTAGTAACAAACTGTAAACCAGTAACTGACAAAATCCACAAAGCATATAAGGACAAAAACAAATATAGGTAAGTAGTACACGCATACTCCCTTTGTTTAGTATAAGAGTAATCACAAAGGTCTGGCTTTTTTATAATTCTACAATATTTTGTCTATTAAGCACTGTTCTAAAATTTATAT		intron_variant	Intron 2 of 3	3		ENSP00000449557.1
GNPTAB	ENST00000549194.1	n.201+112_201+113insTTTCTCATAGCCACCGGTCACTAAAAGTCTAGTAACAAACTGTAAACCAGTAACTGACAAAATCCACAAAGCATATAAGGACAAAAACAAATATAGGTAAGTAGTACACGCATACTCCCTTTGTTTAGTATAAGAGTAATCACAAAGGTCTGGCTTTTTTATAATTCTACAATATTTTGTCTATTAAGCACTGTTCTAAAATTTATAT		intron_variant	Intron 2 of 2	3
GNPTAB	ENST00000549738.5	n.86+112_86+113insTTTCTCATAGCCACCGGTCACTAAAAGTCTAGTAACAAACTGTAAACCAGTAACTGACAAAATCCACAAAGCATATAAGGACAAAAACAAATATAGGTAAGTAGTACACGCATACTCCCTTTGTTTAGTATAAGAGTAATCACAAAGGTCTGGCTTTTTTATAATTCTACAATATTTTGTCTATTAAGCACTGTTCTAAAATTTATAT		intron_variant	Intron 1 of 4	4		ENSP00000450161.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 8

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Pseudo-Hurler polydystrophy;C2673377:Mucolipidosis type II Pathogenic:1

Jan 01, 2016

Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555268712; hg19: chr12-102151237;