2-154450460-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_052917.4(GALNT13):​c.1580C>A​(p.Ser527Tyr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

GALNT13
NM_052917.4 missense

Scores

6
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.42
Variant links:
Genes affected
GALNT13 (HGNC:23242): (polypeptide N-acetylgalactosaminyltransferase 13) The GALNT13 protein is a member of the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAcT; EC 2.4.1.41) family, which initiate O-linked glycosylation of mucins (see MUC3A, MIM 158371) by the initial transfer of N-acetylgalactosamine (GalNAc) with an alpha-linkage to a serine or threonine residue.[supplied by OMIM, Apr 2004]
ENSG00000224675 (HGNC:56700): (GALNT13 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.205358).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GALNT13NM_052917.4 linkc.1580C>A p.Ser527Tyr missense_variant Exon 13 of 13 ENST00000392825.8 NP_443149.2 Q8IUC8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GALNT13ENST00000392825.8 linkc.1580C>A p.Ser527Tyr missense_variant Exon 13 of 13 2 NM_052917.4 ENSP00000376570.3 Q8IUC8-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Dec 10, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1580C>A (p.S527Y) alteration is located in exon 13 (coding exon 11) of the GALNT13 gene. This alteration results from a C to A substitution at nucleotide position 1580, causing the serine (S) at amino acid position 527 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.069
T
BayesDel_noAF
Benign
-0.34
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.19
T
Eigen
Benign
0.17
Eigen_PC
Uncertain
0.36
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Benign
0.85
T
M_CAP
Benign
0.0088
T
MetaRNN
Benign
0.21
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.6
L
PrimateAI
Uncertain
0.73
T
PROVEAN
Benign
-2.1
N
REVEL
Benign
0.12
Sift
Uncertain
0.012
D
Sift4G
Uncertain
0.022
D
Polyphen
0.0020
B
Vest4
0.45
MutPred
0.43
Loss of disorder (P = 0.0306);
MVP
0.16
MPC
0.54
ClinPred
0.60
D
GERP RS
6.0
Varity_R
0.16

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-155306972; API