15-40471616-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_130468.4(CHST14):​c.403C>T​(p.Arg135Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

CHST14
NM_130468.4 missense

Scores

2
12
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.78
Variant links:
Genes affected
CHST14 (HGNC:24464): (carbohydrate sulfotransferase 14) This gene encodes a member of the HNK-1 family of sulfotransferases. The encoded protein transfers sulfate to the C-4 hydroxyl of N-acetylgalactosamine residues in dermatan sulfate. Mutations in this gene have been associated with adducted thumb-clubfoot syndrome.[provided by RefSeq, Mar 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.39207366).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CHST14NM_130468.4 linkc.403C>T p.Arg135Cys missense_variant 1/1 ENST00000306243.7 NP_569735.1 Q8NCH0

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CHST14ENST00000306243.7 linkc.403C>T p.Arg135Cys missense_variant 1/16 NM_130468.4 ENSP00000307297.6 Q8NCH0
CHST14ENST00000559991.1 linkc.403C>T p.Arg135Cys missense_variant 1/25 ENSP00000453882.1 H0YN65

Frequencies

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.75
BayesDel_addAF
Uncertain
0.11
D
BayesDel_noAF
Uncertain
-0.080
CADD
Pathogenic
29
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.30
T;.
Eigen
Uncertain
0.37
Eigen_PC
Uncertain
0.41
FATHMM_MKL
Uncertain
0.86
D
LIST_S2
Uncertain
0.87
D;T
M_CAP
Uncertain
0.092
D
MetaRNN
Benign
0.39
T;T
MetaSVM
Benign
-0.35
T
MutationAssessor
Benign
1.4
L;.
PrimateAI
Uncertain
0.63
T
PROVEAN
Uncertain
-3.5
D;D
REVEL
Uncertain
0.47
Sift
Uncertain
0.0010
D;D
Sift4G
Uncertain
0.0040
D;D
Polyphen
1.0
D;.
Vest4
0.18
MutPred
0.73
Loss of MoRF binding (P = 0.0056);Loss of MoRF binding (P = 0.0056);
MVP
0.66
MPC
2.2
ClinPred
0.98
D
GERP RS
4.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.45
gMVP
0.65

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: rs267606727; hg19: chr15-40763815; API