10-16593417-G-T

Variant names:

• chr10-16593417-G-T
• NM_012425.4:c.811C>A

Variant summary

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

The NM_012425.4(RSU1):​c.811C>A​(p.Pro271Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: RSU1 NM_012425.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 9.60

Genes affected

RSU1 (HGNC:10464): (Ras suppressor protein 1) This gene encodes a protein that is involved in the Ras signal transduction pathway, growth inhibition, and nerve-growth factor induced differentiation processes, as determined in mouse and human cell line studies. In mouse, the encoded protein was initially isolated based on its ability to inhibit v-Ras transformation. Multiple alternatively spliced transcript variants for this gene have been reported; one of these variants was found only in glioma tumors. [provided by RefSeq, Jul 2008]

ACMG classification

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 rank	MANE	Protein	UniProt
RSU1	NM_012425.4	c.811C>A	p.Pro271Thr	missense_variant	Exon 9 of 9	ENST00000345264.10	NP_036557.1
RSU1	NM_152724.3	c.652C>A	p.Pro218Thr	missense_variant	Exon 8 of 8		NP_689937.2
RSU1	XM_047425617.1	c.678C>A	p.Asn226Lys	missense_variant	Exon 7 of 7		XP_047281573.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSU1	ENST00000345264.10	c.811C>A	p.Pro271Thr	missense_variant	Exon 9 of 9	1	NM_012425.4	ENSP00000339521.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jul 12, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.811C>A (p.P271T) alteration is located in exon 9 (coding exon 8) of the RSU1 gene. This alteration results from a C to A substitution at nucleotide position 811, causing the proline (P) at amino acid position 271 to be replaced by a threonine (T). 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	Benign	0.16
BayesDel_addAF	Uncertain	0.072	D
BayesDel_noAF	Benign	-0.13
CADD	Uncertain	25
DANN	Uncertain	0.98
DEOGEN2	Benign	0.018	T;T;.
Eigen	Uncertain	0.54
Eigen_PC	Uncertain	0.62
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.86	.;D;D
M_CAP	Benign	0.021	T
MetaRNN	Uncertain	0.51	D;D;D
MetaSVM	Benign	-0.97	T
PrimateAI	Uncertain	0.69	T
PROVEAN	Benign	-0.68	N;N;.
REVEL	Benign	0.25
Sift	Uncertain	0.010	D;D;.
Sift4G	Benign	0.35	T;T;.
Polyphen		0.98	D;D;.
Vest4		0.65
MutPred		0.22		Gain of phosphorylation at P271 (P = 0.0123);Gain of phosphorylation at P271 (P = 0.0123);.;
MVP		0.71
MPC		0.39
ClinPred		0.98	D
GERP RS		5.2
Varity_R		0.19
gMVP		0.59

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-16635416;