rs1406386033

Variant names:

• chr1-204114339-G-A
• rs1406386033
• NM_005686.3:c.238G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-204114339-G-A
• chr1-204114339-G-C
• chr1-204114339-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005686.3(SOX13):​c.238G>A​(p.Gly80Ser) 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. 14/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G80C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: SOX13 NM_005686.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.890
• Publications: 0 publications found

Genes affected

SOX13 (HGNC:11192): (SRY-box transcription factor 13) 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 cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. It has also been determined to be a type-1 diabetes autoantigen, also known as islet cell antibody 12. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.023798436).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOX13	NM_005686.3	c.238G>A	p.Gly80Ser	missense_variant	Exon 3 of 14	ENST00000367204.6	NP_005677.2
SOX13	XM_047435006.1	c.238G>A	p.Gly80Ser	missense_variant	Exon 3 of 14		XP_047290962.1
SOX13	XM_005245623.4	c.238G>A	p.Gly80Ser	missense_variant	Exon 3 of 14		XP_005245680.1
SOX13	XM_047435007.1	c.238G>A	p.Gly80Ser	missense_variant	Exon 3 of 14		XP_047290963.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX13	ENST00000367204.6	c.238G>A	p.Gly80Ser	missense_variant	Exon 3 of 14	1	NM_005686.3	ENSP00000356172.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD2 exomes AF: 0.00 AC: 0 AN: 239436 AF XY: 0.00

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 FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.066
BayesDel_addAF	Uncertain	0.047	T
BayesDel_noAF	Benign	-0.17
CADD	Benign	14
DANN	Benign	0.39
DEOGEN2	Benign	0.071	T;T;T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.0073	N
LIST_S2	Benign	0.63	.;T;T
M_CAP	Benign	0.036	D
MetaRNN	Benign	0.024	T;T;T
MetaSVM	Uncertain	-0.28	T
MutationAssessor	Benign	-0.81	N;.;N
PhyloP100		0.89
PrimateAI	Benign	0.29	T
PROVEAN	Benign	0.020	N;N;.
REVEL	Uncertain	0.32
Sift	Benign	0.59	T;T;.
Sift4G	Benign	0.67	T;T;T
Polyphen		0.0	B;.;B
Vest4		0.089
MutPred		0.057		Gain of phosphorylation at G80 (P = 0.0166);Gain of phosphorylation at G80 (P = 0.0166);Gain of phosphorylation at G80 (P = 0.0166);
MVP		0.21
MPC		0.028
ClinPred		0.065	T
GERP RS		2.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.037
gMVP		0.039
Mutation Taster		=98/2	polymorphism

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

Other links and lift over

dbSNP: rs1406386033; hg19: chr1-204083467;