18-32208254-A-G

Position:

• chr18-32208254-A-G

Variant summary

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

The NM_005925.3(MEP1B):​c.902A>G​(p.Asn301Ser) 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. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MEP1B NM_005925.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.35

Genes affected

MEP1B (HGNC:7020): (meprin A subunit beta) Meprins are multidomain zinc metalloproteases that are highly expressed in mammalian kidney and intestinal brush border membranes, and in leukocytes and certain cancer cells. They are involved in the hydrolysis of a variety of peptide and protein substrates, and have been implicated in cancer and intestinal inflammation. Mature meprins are oligomers of evolutionarily related, but separately encoded alpha and/or beta subunits. Homooligomers of alpha subunit are secreted, whereas, oligomers containing the beta subunit are plasma membrane-bound. This gene encodes the beta subunit. Targeted disruption of this gene in mice affects embryonic viability, renal gene expression profiles, and distribution of the membrane-associated alpha subunit in kidney and intestine. [provided by RefSeq, Oct 2011]

GAREM1 (HGNC:26136): (GRB2 associated regulator of MAPK1 subtype 1) This gene encodes an adaptor protein which functions in the epidermal growth factor (EGF) receptor-mediated signaling pathway. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

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=0.17257568).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MEP1B	NM_005925.3	c.902A>G	p.Asn301Ser	missense_variant	9/15	ENST00000269202.11	NP_005916.2
MEP1B	NM_001308171.2	c.902A>G	p.Asn301Ser	missense_variant	9/15		NP_001295100.1
MEP1B	XM_011526013.3	c.683A>G	p.Asn228Ser	missense_variant	8/14		XP_011524315.1
MEP1B	XM_011526014.3	c.548-2247A>G		intron_variant			XP_011524316.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEP1B	ENST00000269202.11	c.902A>G	p.Asn301Ser	missense_variant	9/15	1	NM_005925.3	ENSP00000269202	P4
MEP1B	ENST00000581447.1	c.902A>G	p.Asn301Ser	missense_variant	9/15	1		ENSP00000463280	A1
GAREM1	ENST00000583696.1	c.66-71794T>C		intron_variant		3		ENSP00000464185

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 27, 2023

The c.902A>G (p.N301S) alteration is located in exon 9 (coding exon 9) of the MEP1B gene. This alteration results from a A to G substitution at nucleotide position 902, causing the asparagine (N) at amino acid position 301 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	18
DANN	Uncertain	0.99
DEOGEN2	Benign	0.11	T;T
Eigen	Benign	-0.12
Eigen_PC	Benign	0.00095
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.64	T;T
M_CAP	Benign	0.0073	T
MetaRNN	Benign	0.17	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.4	M;.
MutationTaster	Benign	0.90	N;N
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-1.9	N;.
REVEL	Benign	0.19
Sift	Benign	0.41	T;.
Sift4G	Benign	0.41	T;T
Polyphen		0.29	B;.
Vest4		0.10
MutPred		0.37		Gain of phosphorylation at N301 (P = 0.0595);Gain of phosphorylation at N301 (P = 0.0595);
MVP		0.47
MPC		0.11
ClinPred		0.74	D
GERP RS		4.3
Varity_R		0.26
gMVP		0.52

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-29788217; COSMIC: COSV99328740; COSMIC: COSV99328740;