18-32202916-C-T

Variant names:

• chr18-32202916-C-T
• NM_005925.3:c.274C>T

Variant summary

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

The NM_005925.3(MEP1B):​c.274C>T​(p.Leu92Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 1.77

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 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
MEP1B	NM_005925.3	c.274C>T	p.Leu92Phe	missense_variant	Exon 6 of 15	ENST00000269202.11	NP_005916.2
MEP1B	NM_001308171.2	c.274C>T	p.Leu92Phe	missense_variant	Exon 6 of 15		NP_001295100.1
MEP1B	XM_011526013.3	c.274C>T	p.Leu92Phe	missense_variant	Exon 6 of 14		XP_011524315.1
MEP1B	XM_011526014.3	c.274C>T	p.Leu92Phe	missense_variant	Exon 6 of 13		XP_011524316.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEP1B	ENST00000269202.11	c.274C>T	p.Leu92Phe	missense_variant	Exon 6 of 15	1	NM_005925.3	ENSP00000269202.6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Dec 14, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.274C>T (p.L92F) alteration is located in exon 6 (coding exon 6) of the MEP1B gene. This alteration results from a C to T substitution at nucleotide position 274, causing the leucine (L) at amino acid position 92 to be replaced by a phenylalanine (F). 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	0.13
BayesDel_addAF	Uncertain	0.088	D
BayesDel_noAF	Benign	-0.11
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.54	D;D;D
Eigen	Uncertain	0.47
Eigen_PC	Uncertain	0.50
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Benign	0.84	T;D;D
M_CAP	Benign	0.022	T
MetaRNN	Uncertain	0.62	D;D;D
MetaSVM	Benign	-0.50	T
MutationAssessor	Pathogenic	3.2	.;M;.
PrimateAI	Uncertain	0.62	T
PROVEAN	Uncertain	-3.2	.;D;.
REVEL	Uncertain	0.33
Sift	Benign	0.034	.;D;.
Sift4G	Benign	0.34	T;T;T
Polyphen		0.76	.;P;.
Vest4		0.65, 0.65
MutPred		0.60		.;Gain of ubiquitination at K88 (P = 0.1317);Gain of ubiquitination at K88 (P = 0.1317);
MVP		0.62
MPC		0.41
ClinPred		0.99	D
GERP RS		4.8
Varity_R		0.37
gMVP		0.67

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-29782879;