rs267606728

Variant summary

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

The NM_130468.4(CHST14):​c.410T>A​(p.Leu137Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as no classification for the single variant (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

CHST14
NM_130468.4 missense

Scores

3
11
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.24
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 2 ACMG points.

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

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CHST14NM_130468.4 linkc.410T>A p.Leu137Gln 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.410T>A p.Leu137Gln missense_variant 1/16 NM_130468.4 ENSP00000307297.6 Q8NCH0
CHST14ENST00000559991.1 linkc.410T>A p.Leu137Gln 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
0.90
BayesDel_addAF
Pathogenic
0.39
D
BayesDel_noAF
Pathogenic
0.33
CADD
Pathogenic
28
DANN
Uncertain
1.0
DEOGEN2
Benign
0.22
T;.
Eigen
Uncertain
0.35
Eigen_PC
Uncertain
0.36
FATHMM_MKL
Benign
0.71
D
LIST_S2
Uncertain
0.87
D;T
M_CAP
Uncertain
0.088
D
MetaRNN
Uncertain
0.54
D;D
MetaSVM
Benign
-0.58
T
MutationAssessor
Benign
1.9
L;.
PrimateAI
Uncertain
0.59
T
PROVEAN
Uncertain
-2.6
D;D
REVEL
Uncertain
0.64
Sift
Uncertain
0.0010
D;D
Sift4G
Uncertain
0.0040
D;D
Polyphen
1.0
D;.
Vest4
0.38
MutPred
0.78
Loss of stability (P = 0.0202);Loss of stability (P = 0.0202);
MVP
1.0
MPC
2.0
ClinPred
0.97
D
GERP RS
4.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.67
gMVP
0.56

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: rs267606728; hg19: chr15-40763822; API