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GeneBe

9-127896279-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_013443.5(ST6GALNAC6):​c.80C>A​(p.Pro27His) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

ST6GALNAC6
NM_013443.5 missense

Scores

5
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.29
Variant links:
Genes affected
ST6GALNAC6 (HGNC:23364): (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 6) ST6GALNAC6 belongs to a family of sialyltransferases that modify proteins and ceramides on the cell surface to alter cell-cell or cell-extracellular matrix interactions (Tsuchida et al., 2003 [PubMed 12668675]).[supplied by OMIM, Mar 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ST6GALNAC6NM_013443.5 linkuse as main transcriptc.80C>A p.Pro27His missense_variant 3/7 ENST00000373146.6
ST6GALNAC4-ST6GALNAC6-AK1NR_174625.1 linkuse as main transcriptn.956C>A non_coding_transcript_exon_variant 5/15

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ST6GALNAC6ENST00000373146.6 linkuse as main transcriptc.80C>A p.Pro27His missense_variant 3/71 NM_013443.5 Q969X2-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMar 01, 2023The c.80C>A (p.P27H) alteration is located in exon 3 (coding exon 2) of the ST6GALNAC6 gene. This alteration results from a C to A substitution at nucleotide position 80, causing the proline (P) at amino acid position 27 to be replaced by a histidine (H). 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
0.10
BayesDel_addAF
Benign
-0.051
T
BayesDel_noAF
Benign
-0.31
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.017
T;T;.
Eigen
Benign
0.17
Eigen_PC
Benign
0.13
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Benign
0.71
T;.;T
M_CAP
Benign
0.012
T
MetaRNN
Uncertain
0.45
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.55
N;N;N
MutationTaster
Benign
1.0
D;D;D;N;N;N
PrimateAI
Benign
0.45
T
PROVEAN
Benign
-0.15
N;N;N
REVEL
Benign
0.15
Sift
Uncertain
0.0010
D;D;D
Sift4G
Uncertain
0.017
D;D;D
Polyphen
0.98
D;D;.
Vest4
0.62
MutPred
0.24
Loss of glycosylation at P27 (P = 0.0123);Loss of glycosylation at P27 (P = 0.0123);Loss of glycosylation at P27 (P = 0.0123);
MVP
0.52
MPC
1.5
ClinPred
0.65
D
GERP RS
3.5
Varity_R
0.10
gMVP
0.29

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: chr9-130658558; API