rs750752125

Variant names:

• chr7-40133067-A-C
• rs750752125
• NM_138701.4:c.532T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-40133067-A-C
• chr7-40133067-A-G

Variant summary

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

The NM_138701.4(MPLKIP):​c.532T>G​(p.Phe178Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MPLKIP NM_138701.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.20

Genes affected

MPLKIP (HGNC:16002): (M-phase specific PLK1 interacting protein) The protein encoded by this gene localizes to the centrosome during mitosis and to the midbody during cytokinesis. The protein is phosphorylated by cyclin-dependent kinase 1 during mitosis and subsequently interacts with polo-like kinase 1. The protein is thought to function in regulating mitosis and cytokinesis. Mutations in this gene result in nonphotosensitive trichothiodystrophy. [provided by RefSeq, Nov 2009]

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
MPLKIP	NM_138701.4	c.532T>G	p.Phe178Val	missense_variant	Exon 2 of 2	ENST00000306984.8	NP_619646.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPLKIP	ENST00000306984.8	c.532T>G	p.Phe178Val	missense_variant	Exon 2 of 2	1	NM_138701.4	ENSP00000304553.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.82
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.21
CADD	Pathogenic	26
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.49	T;T
Eigen	Uncertain	0.26
Eigen_PC	Uncertain	0.34
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.53	.;T
M_CAP	Uncertain	0.17	D
MetaRNN	Uncertain	0.45	T;T
MetaSVM	Uncertain	-0.085	T
MutationAssessor	Benign	0.90	L;L
PrimateAI	Uncertain	0.71	T
PROVEAN	Benign	-1.8	N;.
REVEL	Uncertain	0.60
Sift	Uncertain	0.0040	D;.
Sift4G	Uncertain	0.0080	D;.
Polyphen		0.57	P;P
Vest4		0.68
MutPred		0.32		Gain of MoRF binding (P = 0.0667);Gain of MoRF binding (P = 0.0667);
MVP		0.81
MPC		1.1
ClinPred		0.84	D
GERP RS		4.4
Varity_R		0.25
gMVP		0.51

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

Other links and lift over

dbSNP: rs750752125; hg19: chr7-40172666;