7-129456596-T-C

Variant names:

• chr7-129456596-T-C
• rs375374382
• NM_020704.3:c.992T>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_020704.3(STRIP2):​c.992T>C​(p.Leu331Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts 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. L331R) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 30)
• Consequence: STRIP2 NM_020704.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.45
• Publications: 0 publications found

Genes affected

STRIP2 (HGNC:22209): (striatin interacting protein 2) Involved in cell migration; cytoskeleton organization; and regulation of cell shape. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

STRIP2 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.23867506).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020704.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRIP2	NM_020704.3	MANE Select	c.992T>C	p.Leu331Pro	missense	Exon 9 of 21	NP_065755.1	Q9ULQ0-1
	STRIP2	NM_001134336.2		c.992T>C	p.Leu331Pro	missense	Exon 9 of 20	NP_001127808.1	Q9ULQ0-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRIP2	ENST00000249344.7	TSL:1 MANE Select	c.992T>C	p.Leu331Pro	missense	Exon 9 of 21	ENSP00000249344.2	Q9ULQ0-1
	STRIP2	ENST00000435494.2	TSL:1	c.992T>C	p.Leu331Pro	missense	Exon 9 of 20	ENSP00000392393.2	Q9ULQ0-2
	STRIP2	ENST00000947594.1		c.920T>C	p.Leu307Pro	missense	Exon 9 of 21	ENSP00000617653.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.091
BayesDel_addAF	Benign	-0.0030	T
BayesDel_noAF	Benign	-0.24
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.011	T
Eigen	Uncertain	0.24
Eigen_PC	Uncertain	0.36
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.74	T
M_CAP	Benign	0.0063	T
MetaRNN	Benign	0.24	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.34	N
PhyloP100		4.4
PrimateAI	Uncertain	0.63	T
PROVEAN	Benign	-0.70	N
REVEL	Benign	0.11
Sift	Benign	0.22	T
Sift4G	Benign	0.20	T
Polyphen		0.80	P
Vest4		0.62
MutPred		0.39		Loss of helix (P = 0.0123)
MVP		0.40
MPC		0.58
ClinPred		0.75	D
GERP RS		5.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.18
gMVP		0.084
Mutation Taster		=71/29	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: rs375374382; hg19: chr7-129096437;