GeneBe

rs111033640

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000605275.1(GALT):​n.209-101_209-94delCAGTCAGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000939 in 1,065,102 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 9.4e-7 ( 0 hom. )

Consequence

GALT
ENST00000605275.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.263

Publications

0 publications found
Variant links:
Genes affected
GALT (HGNC:4135): (galactose-1-phosphate uridylyltransferase) Galactose-1-phosphate uridyl transferase (GALT) catalyzes the second step of the Leloir pathway of galactose metabolism, namely the conversion of UDP-glucose + galactose-1-phosphate to glucose-1-phosphate + UDP-galactose. The absence of this enzyme results in classic galactosemia in humans and can be fatal in the newborn period if lactose is not removed from the diet. The pathophysiology of galactosemia has not been clearly defined. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
GALT Gene-Disease associations (from GenCC):
  • classic galactosemia
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
  • galactosemia
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen, Myriad Women’s Health

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ACMG classification

Classification was made for transcript

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

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GALTNM_000155.4 linkc.-129_-122delCAGTCAGT upstream_gene_variant ENST00000378842.8 NP_000146.2 P07902-1B2RAT6A0A0S2Z3Y7
GALTNM_001258332.2 linkc.-331_-324delCAGTCAGT upstream_gene_variant NP_001245261.1 P07902-2B2RAT6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GALTENST00000378842.8 linkc.-129_-122delCAGTCAGT upstream_gene_variant 1 NM_000155.4 ENSP00000368119.4 P07902-1
ENSG00000258728ENST00000556278.1 linkc.-129_-122delCAGTCAGT upstream_gene_variant 5 ENSP00000451792.1 G3V4G9

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
9.39e-7
AC:
1
AN:
1065102
Hom.:
0
AF XY:
0.00000184
AC XY:
1
AN XY:
544704
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
25418
American (AMR)
AF:
0.00
AC:
0
AN:
39784
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
23272
East Asian (EAS)
AF:
0.00
AC:
0
AN:
36074
South Asian (SAS)
AF:
0.00
AC:
0
AN:
76240
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
50416
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3434
European-Non Finnish (NFE)
AF:
0.00000131
AC:
1
AN:
763372
Other (OTH)
AF:
0.00
AC:
0
AN:
47092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.26

Splicing

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

Publications

Other links and lift over

dbSNP: rs111033640; hg19: chr9-34646572; API