rs201009720

Variant names:

• chr3-38246135-C-G
• rs201009720
• NM_005109.3:c.1171C>G

Your query was ambiguous. Multiple possible variants found:

• chr3-38246135-C-G
• chr3-38246135-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_005109.3(OXSR1):​c.1171C>G​(p.His391Asp) 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. 15/21 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. H391Y) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: OXSR1 NM_005109.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

Genes affected

OXSR1 (HGNC:8508): (oxidative stress responsive kinase 1) The product of this gene belongs to the Ser/Thr protein kinase family of proteins. It regulates downstream kinases in response to environmental stress, and may play a role in regulating the actin cytoskeleton. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13209793).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OXSR1	NM_005109.3	c.1171C>G	p.His391Asp	missense_variant	Exon 13 of 18	ENST00000311806.8	NP_005100.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OXSR1	ENST00000311806.8	c.1171C>G	p.His391Asp	missense_variant	Exon 13 of 18	1	NM_005109.3	ENSP00000311713.3
OXSR1	ENST00000446845.5	c.1171C>G	p.His391Asp	missense_variant	Exon 13 of 15	5		ENSP00000415851.1
OXSR1	ENST00000467900.1	n.398C>G		non_coding_transcript_exon_variant	Exon 3 of 6	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.084
BayesDel_addAF	Benign	-0.024	T
BayesDel_noAF	Benign	-0.27
CADD	Benign	19
DANN	Uncertain	0.98
DEOGEN2	Benign	0.035	.;T
Eigen	Benign	-0.11
Eigen_PC	Benign	0.099
FATHMM_MKL	Uncertain	0.81	D
LIST_S2	Benign	0.75	T;T
M_CAP	Benign	0.0092	T
MetaRNN	Benign	0.13	T;T
MetaSVM	Benign	-0.76	T
MutationAssessor	Benign	1.0	.;L
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-0.67	N;N
REVEL	Benign	0.16
Sift	Benign	0.59	T;T
Sift4G	Benign	0.63	T;T
Polyphen		0.0050	.;B
Vest4		0.28
MutPred		0.20		Loss of glycosylation at P393 (P = 0.0998);Loss of glycosylation at P393 (P = 0.0998);
MVP		0.60
MPC		1.0
ClinPred		0.24	T
GERP RS		5.7
Varity_R		0.083
gMVP		0.17

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs201009720; hg19: chr3-38287626; COSMIC: COSV61258841;