rs546671806

Variant names:

• chr5-66596991-C-G
• rs546671806
• NM_001164664.2:c.336C>G

Your query was ambiguous. Multiple possible variants found:

• chr5-66596991-C-G
• chr5-66596991-C-T

Variant summary

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

The NM_001164664.2(MAST4):​c.336C>G​(p.Ser112Arg) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S112S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MAST4 NM_001164664.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

Genes affected

MAST4 (HGNC:19037): (microtubule associated serine/threonine kinase family member 4) This gene encodes a member of the microtubule-associated serine/threonine protein kinases. The proteins in this family contain a domain that gives the kinase the ability to determine its own scaffold to control the effects of their kinase activities. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2014]

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=0.19612363).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAST4	NM_001164664.2	c.336C>G	p.Ser112Arg	missense_variant	Exon 1 of 29	ENST00000403625.7	NP_001158136.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAST4	ENST00000403625.7	c.336C>G	p.Ser112Arg	missense_variant	Exon 1 of 29	5	NM_001164664.2	ENSP00000385727.1
MAST4	ENST00000406374.5	c.336C>G	p.Ser112Arg	missense_variant	Exon 1 of 6	1		ENSP00000385088.1
MAST4	ENST00000406039.5	c.336C>G	p.Ser112Arg	missense_variant	Exon 1 of 5	1		ENSP00000384547.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.42
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.0058	T;.;T
Eigen	Benign	-0.055
Eigen_PC	Benign	-0.066
FATHMM_MKL	Uncertain	0.77	D
LIST_S2	Benign	0.73	T;T;T
M_CAP	Pathogenic	0.52	D
MetaRNN	Benign	0.20	T;T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	0.55	N;N;.
PrimateAI	Pathogenic	0.88	D
PROVEAN	Benign	-0.36	N;N;N
REVEL	Benign	0.12
Sift	Uncertain	0.014	D;D;D
Sift4G	Benign	0.20	T;T;T
Polyphen		0.99	.;D;D
Vest4		0.20
MutPred		0.15		Loss of phosphorylation at S112 (P = 0.0047);Loss of phosphorylation at S112 (P = 0.0047);Loss of phosphorylation at S112 (P = 0.0047);
MVP		0.80
MPC		1.1
ClinPred		0.70	D
GERP RS		2.8
Varity_R		0.17
gMVP		0.082

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs546671806; hg19: chr5-65892819;