rs1405825332

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-27025887-A-G
• chr2-27025887-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 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

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

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=0.24450508).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAPRE3	NM_012326.4	c.632A>G	p.Asp211Gly	missense_variant	Exon 6 of 7	ENST00000233121.7	NP_036458.2
MAPRE3	NM_001303050.2	c.632A>G	p.Asp211Gly	missense_variant	Exon 6 of 7		NP_001289979.1
MAPRE3	NM_001410716.1	c.587A>G	p.Asp196Gly	missense_variant	Exon 6 of 7		NP_001397645.1
MAPRE3	XM_047443728.1	c.632A>G	p.Asp211Gly	missense_variant	Exon 6 of 7		XP_047299684.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAPRE3	ENST00000233121.7	c.632A>G	p.Asp211Gly	missense_variant	Exon 6 of 7	1	NM_012326.4	ENSP00000233121.2

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	0.38
BayesDel_addAF	Benign	-0.092	T
BayesDel_noAF	Benign	-0.37
CADD	Pathogenic	26
DANN	Benign	0.96
DEOGEN2	Benign	0.23	T;.;.;T;.
Eigen	Benign	-0.27
Eigen_PC	Benign	-0.20
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.90	D;.;.;D;D
M_CAP	Benign	0.020	T
MetaRNN	Benign	0.24	T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.1	M;.;.;.;.
PrimateAI	Uncertain	0.62	T
PROVEAN	Uncertain	-2.5	D;D;.;N;D
REVEL	Benign	0.15
Sift	Benign	0.12	T;T;.;T;T
Sift4G	Uncertain	0.032	D;D;.;T;D
Polyphen		0.019	B;B;B;.;B
Vest4		0.54
MutPred		0.32		Loss of stability (P = 0.092);.;.;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

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

Publications

LitVar

Other links and lift over

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