GeneBe

rs76300806

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_024312.5(GNPTAB):​c.-53_-39delGGCGGCGGCGGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000111 in 897,540 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000011 ( 0 hom. )

Consequence

GNPTAB
NM_024312.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.20

Publications

0 publications found
Variant links:
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: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia, Genomics England PanelApp
  • mucolipidosis type III, alpha/beta
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, G2P, Genomics England PanelApp

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GNPTABNM_024312.5 linkc.-53_-39delGGCGGCGGCGGCGGC 5_prime_UTR_variant Exon 1 of 21 ENST00000299314.12 NP_077288.2
GNPTABXM_006719593.4 linkc.-53_-39delGGCGGCGGCGGCGGC 5_prime_UTR_variant Exon 1 of 19 XP_006719656.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GNPTABENST00000299314.12 linkc.-53_-39delGGCGGCGGCGGCGGC 5_prime_UTR_variant Exon 1 of 21 1 NM_024312.5 ENSP00000299314.7

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000111
AC:
1
AN:
897540
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
464972
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
17692
American (AMR)
AF:
0.00
AC:
0
AN:
35184
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20934
East Asian (EAS)
AF:
0.0000329
AC:
1
AN:
30358
South Asian (SAS)
AF:
0.00
AC:
0
AN:
69034
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
47034
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3096
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
634302
Other (OTH)
AF:
0.00
AC:
0
AN:
39906
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.2

Splicing

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

Publications

Other links and lift over

dbSNP: rs76300806; hg19: chr12-102224491; API