X-140503818-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_005634.3(SOX3):​c.1243G>A​(p.Ala415Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,176,717 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000044 ( 0 hom., 0 hem., cov: 23)
Exomes 𝑓: 0.000013 ( 0 hom. 5 hem. )

Consequence

SOX3
NM_005634.3 missense

Scores

2
1
14

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.751
Variant links:
Genes affected
SOX3 (HGNC:11199): (SRY-box transcription factor 3) This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. Mutations in this gene have been associated with X-linked cognitive disability with growth hormone deficiency. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.24435994).
BP6
Variant X-140503818-C-T is Benign according to our data. Variant chrX-140503818-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3389294.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAdExome4 at 5 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SOX3NM_005634.3 linkc.1243G>A p.Ala415Thr missense_variant Exon 1 of 1 ENST00000370536.5 NP_005625.2 P41225

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SOX3ENST00000370536.5 linkc.1243G>A p.Ala415Thr missense_variant Exon 1 of 1 6 NM_005634.3 ENSP00000359567.2 P41225

Frequencies

GnomAD3 genomes
AF:
0.0000445
AC:
5
AN:
112483
Hom.:
0
Cov.:
23
AF XY:
0.00
AC XY:
0
AN XY:
34675
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000942
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000132
AC:
14
AN:
1064234
Hom.:
0
Cov.:
32
AF XY:
0.0000145
AC XY:
5
AN XY:
345278
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:
0.0000156
Gnomad4 OTH exome
AF:
0.0000222
GnomAD4 genome
AF:
0.0000445
AC:
5
AN:
112483
Hom.:
0
Cov.:
23
AF XY:
0.00
AC XY:
0
AN XY:
34675
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000942
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000594
Hom.:
2

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Nov 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

SOX3: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.073
BayesDel_addAF
Benign
-0.38
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
20
DANN
Uncertain
0.99
DEOGEN2
Benign
0.37
T
FATHMM_MKL
Benign
0.47
N
LIST_S2
Benign
0.48
T
M_CAP
Pathogenic
0.85
D
MetaRNN
Benign
0.24
T
MetaSVM
Benign
-0.63
T
MutationAssessor
Benign
0.82
L
PrimateAI
Pathogenic
0.83
D
PROVEAN
Benign
-1.3
N
REVEL
Benign
0.15
Sift
Benign
0.036
D
Sift4G
Benign
0.20
T
Polyphen
0.77
P
Vest4
0.11
MutPred
0.17
Gain of relative solvent accessibility (P = 0.005);
MVP
0.33
ClinPred
0.47
T
GERP RS
2.6
Varity_R
0.20
gMVP
0.46

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: rs1273198624; hg19: chrX-139585983; COSMIC: COSV65167864; API