rs1555268712

Variant names:

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

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. 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. 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. 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
• Publications: 0 publications found

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]

GNPTAB Gene-Disease associations (from GenCC):

• GNPTAB-mucolipidosis

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• mucolipidosis

  Inheritance: AR Classification: DEFINITIVE Submitted by: Myriad Women’s Health
• mucolipidosis type II

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Genomics England PanelApp, Orphanet, Labcorp Genetics (formerly Invitae)
• mucolipidosis type III, alpha/beta

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Genomics England PanelApp, Orphanet, Ambry Genetics

ACMG classification

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

• 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 VariationId is 397571.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024312.5. 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
	GNPTAB	NM_024312.5	MANE Select	c.3250-10_3335+112dupTTTCTCATAGCCACCGGTCACTAAAAGTCTAGTAACAAACTGTAAACCAGTAACTGACAAAATCCACAAAGCATATAAGGACAAAAACAAATATAGGTAAGTAGTACACGCATACTCCCTTTGTTTAGTATAAGAGTAATCACAAAGGTCTGGCTTTTTTATAATTCTACAATATTTTGTCTATTAAGCACTGTTCTAAAATTTATAT		intron	N/A	NP_077288.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNPTAB	ENST00000299314.12	TSL:1 MANE Select	c.3335+112_3335+113insTTTCTCATAGCCACCGGTCACTAAAAGTCTAGTAACAAACTGTAAACCAGTAACTGACAAAATCCACAAAGCATATAAGGACAAAAACAAATATAGGTAAGTAGTACACGCATACTCCCTTTGTTTAGTATAAGAGTAATCACAAAGGTCTGGCTTTTTTATAATTCTACAATATTTTGTCTATTAAGCACTGTTCTAAAATTTATAT		intron	N/A	ENSP00000299314.7	Q3T906-1
	GNPTAB	ENST00000917136.1		c.3356+112_3356+113insTTTCTCATAGCCACCGGTCACTAAAAGTCTAGTAACAAACTGTAAACCAGTAACTGACAAAATCCACAAAGCATATAAGGACAAAAACAAATATAGGTAAGTAGTACACGCATACTCCCTTTGTTTAGTATAAGAGTAATCACAAAGGTCTGGCTTTTTTATAATTCTACAATATTTTGTCTATTAAGCACTGTTCTAAAATTTATAT		intron	N/A	ENSP00000587195.1
	GNPTAB	ENST00000917134.1		c.3329+112_3329+113insTTTCTCATAGCCACCGGTCACTAAAAGTCTAGTAACAAACTGTAAACCAGTAACTGACAAAATCCACAAAGCATATAAGGACAAAAACAAATATAGGTAAGTAGTACACGCATACTCCCTTTGTTTAGTATAAGAGTAATCACAAAGGTCTGGCTTTTTTATAATTCTACAATATTTTGTCTATTAAGCACTGTTCTAAAATTTATAT		intron	N/A	ENSP00000587193.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 8

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Likely pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Pseudo-Hurler polydystrophy;C2673377:Mucolipidosis type II (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1555268712; hg19: chr12-102151237;