chr4-69854239-G-A

Variant summary

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

The NM_005420.3(SULT1E1):​c.347C>T​(p.Ser116Leu) 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: 33)

Consequence

SULT1E1
NM_005420.3 missense

Scores

5
11
3

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.01
Variant links:
Genes affected
SULT1E1 (HGNC:11377): (sulfotransferase family 1E member 1) Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These cytosolic enzymes are different in their tissue distributions and substrate specificities. The gene structure (number and length of exons) is similar among family members. This gene encodes a protein that transfers a sulfo moiety to and from estrone, which may control levels of estrogen receptors. [provided by RefSeq, Jul 2008]

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/exons MANE UniProt
SULT1E1NM_005420.3 linkuse as main transcriptc.347C>T p.Ser116Leu missense_variant 4/8 ENST00000226444.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SULT1E1ENST00000226444.4 linkuse as main transcriptc.347C>T p.Ser116Leu missense_variant 4/81 NM_005420.3 P1
SULT1E1ENST00000504002.1 linkuse as main transcriptn.453C>T non_coding_transcript_exon_variant 4/51

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000399
AC:
1
AN:
250872
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135622
show subpopulations
Gnomad AFR exome
AF:
0.0000616
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:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.0000151
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.00
AC:
0

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 15, 2024The c.347C>T (p.S116L) alteration is located in exon 4 (coding exon 3) of the SULT1E1 gene. This alteration results from a C to T substitution at nucleotide position 347, causing the serine (S) at amino acid position 116 to be replaced by a leucine (L). 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
Uncertain
0.46
BayesDel_addAF
Pathogenic
0.19
D
BayesDel_noAF
Uncertain
0.040
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.85
D
Eigen
Pathogenic
0.71
Eigen_PC
Uncertain
0.62
FATHMM_MKL
Benign
0.73
D
LIST_S2
Uncertain
0.92
D
M_CAP
Benign
0.035
D
MetaRNN
Uncertain
0.67
D
MetaSVM
Uncertain
0.29
D
MutationAssessor
Pathogenic
3.1
M
MutationTaster
Benign
0.90
N
PrimateAI
Uncertain
0.53
T
PROVEAN
Pathogenic
-4.9
D
REVEL
Uncertain
0.56
Sift
Uncertain
0.023
D
Sift4G
Uncertain
0.021
D
Polyphen
0.86
P
Vest4
0.39
MVP
0.97
MPC
0.34
ClinPred
0.99
D
GERP RS
3.8
Varity_R
0.72
gMVP
0.57

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.090
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: rs369730845; hg19: chr4-70719957; API