NM_012326.4:c.632A>G

Variant names:

• chr2-27025887-A-G
• rs1405825332
• NM_012326.4:c.632A>G

Variant summary

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

The NM_012326.4(MAPRE3):​c.632A>G​(p.Asp211Gly) 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. D211V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MAPRE3 NM_012326.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.30
• Publications: 0 publications found

Genes affected

MAPRE3 (HGNC:6892): (microtubule associated protein RP/EB family member 3) The protein encoded by this gene is a member of the RP/EB family of genes. The protein localizes to the cytoplasmic microtubule network and binds APCL, a homolog of the adenomatous polyposis coli tumor suppressor gene. [provided by RefSeq, Jul 2008]

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=0.24450508).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012326.4. 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
	MAPRE3	NM_012326.4	MANE Select	c.632A>G	p.Asp211Gly	missense	Exon 6 of 7	NP_036458.2
	MAPRE3	NM_001303050.2		c.632A>G	p.Asp211Gly	missense	Exon 6 of 7	NP_001289979.1	Q9UPY8-1
	MAPRE3	NM_001410716.1		c.587A>G	p.Asp196Gly	missense	Exon 6 of 7	NP_001397645.1	Q9UPY8-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPRE3	ENST00000233121.7	TSL:1 MANE Select	c.632A>G	p.Asp211Gly	missense	Exon 6 of 7	ENSP00000233121.2	Q9UPY8-1
	MAPRE3	ENST00000879840.1		c.635A>G	p.Asp212Gly	missense	Exon 6 of 7	ENSP00000549899.1
	MAPRE3	ENST00000879843.1		c.632A>G	p.Asp211Gly	missense	Exon 6 of 7	ENSP00000549902.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.38
BayesDel_addAF	Benign	-0.092	T
BayesDel_noAF	Benign	-0.37
CADD	Pathogenic	26
DANN	Benign	0.96
DEOGEN2	Benign	0.23	T
Eigen	Benign	-0.27
Eigen_PC	Benign	-0.20
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.90	D
M_CAP	Benign	0.020	T
MetaRNN	Benign	0.24	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		4.3
PrimateAI	Uncertain	0.62	T
PROVEAN	Uncertain	-2.5	D
REVEL	Benign	0.15
Sift	Benign	0.12	T
Sift4G	Uncertain	0.032	D
Polyphen		0.019	B
Vest4		0.54
MutPred		0.32		Loss of stability (P = 0.092)
MVP		0.63
MPC		1.1
ClinPred		0.71	D
GERP RS		3.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.28
gMVP		0.75
Mutation Taster		=56/44	polymorphism

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

Other links and lift over

dbSNP: rs1405825332; hg19: chr2-27248755; COSMIC: COSV51866444; COSMIC: COSV51866444;