rs149340486

Variant summary

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

The NM_001011551.3(C1GALT1C1):​c.302G>T​(p.Ser101Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000000911 in 1,097,925 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 23)
Exomes 𝑓: 9.1e-7 ( 0 hom. 0 hem. )

Consequence

C1GALT1C1
NM_001011551.3 missense

Scores

4
9
4

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.70
Variant links:
Genes affected
C1GALT1C1 (HGNC:24338): (C1GALT1 specific chaperone 1) This gene encodes a type II transmembrane protein that is similar to the core 1 beta1,3-galactosyltransferase 1, which catalyzes the synthesis of the core-1 structure, also known as Thomsen-Friedenreich antigen, on O-linked glycans. This gene product lacks the galactosyltransferase activity itself, but instead acts as a molecular chaperone required for the folding, stability and full activity of the core 1 beta1,3-galactosyltransferase 1. Mutations in this gene have been associated with Tn syndrome. Alternatively spliced transcript variants encoding the same protein have been identified. [provided by RefSeq, Dec 2009]

Genome browser will be placed here

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 rank MANE Protein UniProt
C1GALT1C1NM_001011551.3 linkc.302G>T p.Ser101Ile missense_variant Exon 2 of 2 ENST00000304661.6 NP_001011551.1 Q96EU7
C1GALT1C1NM_152692.5 linkc.302G>T p.Ser101Ile missense_variant Exon 3 of 3 NP_689905.1 Q96EU7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C1GALT1C1ENST00000304661.6 linkc.302G>T p.Ser101Ile missense_variant Exon 2 of 2 1 NM_001011551.3 ENSP00000304364.5 Q96EU7
C1GALT1C1ENST00000371313.2 linkc.302G>T p.Ser101Ile missense_variant Exon 3 of 3 1 ENSP00000360363.2 Q96EU7

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD3 exomes
AF:
0.00000547
AC:
1
AN:
182742
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
67270
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000122
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
9.11e-7
AC:
1
AN:
1097925
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
363309
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000119
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.87
BayesDel_addAF
Pathogenic
0.20
D
BayesDel_noAF
Uncertain
0.050
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.65
D;D
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Benign
0.85
.;T
M_CAP
Benign
0.065
D
MetaRNN
Uncertain
0.71
D;D
MetaSVM
Benign
-0.33
T
MutationAssessor
Pathogenic
3.5
M;M
PrimateAI
Uncertain
0.49
T
PROVEAN
Pathogenic
-5.4
D;D
REVEL
Uncertain
0.41
Sift
Uncertain
0.0020
D;D
Sift4G
Uncertain
0.019
D;D
Polyphen
0.91
P;P
Vest4
0.63
MutPred
0.70
Loss of disorder (P = 0.0174);Loss of disorder (P = 0.0174);
MVP
0.64
MPC
0.84
ClinPred
0.97
D
GERP RS
5.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.91
gMVP
0.92

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs149340486; hg19: chrX-119760720; API