X-107841225-A-G

Position:

• chrX-107841225-A-G

Variant summary

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

The NM_012216.4(MID2):​c.560A>G​(p.Asp187Gly) variant causes a missense change involving the alteration of a 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: 23)
• Consequence: MID2 NM_012216.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 8.95

Genes affected

MID2 (HGNC:7096): (midline 2) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to microtubular structures in the cytoplasm. Alternate splicing of this gene results in two transcript variants encoding different isoforms. [provided by RefSeq, Feb 2009]

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/exons	MANE	Protein	UniProt
MID2	NM_012216.4	c.560A>G	p.Asp187Gly	missense_variant	2/10	ENST00000262843.11	NP_036348.2
MID2	NM_001382751.1	c.500A>G	p.Asp167Gly	missense_variant	2/10		NP_001369680.1
MID2	NM_052817.3	c.560A>G	p.Asp187Gly	missense_variant	2/10		NP_438112.2
MID2	NM_001382752.1	c.500A>G	p.Asp167Gly	missense_variant	2/10		NP_001369681.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MID2	ENST00000262843.11	c.560A>G	p.Asp187Gly	missense_variant	2/10	1	NM_012216.4	ENSP00000262843.6
MID2	ENST00000443968.2	c.560A>G	p.Asp187Gly	missense_variant	2/10	1		ENSP00000413976.2
MID2	ENST00000451923.1	c.500A>G	p.Asp167Gly	missense_variant	2/2	3		ENSP00000410730.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 23

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

Dec 15, 2022

The c.560A>G (p.D187G) alteration is located in exon 2 (coding exon 2) of the MID2 gene. This alteration results from a A to G substitution at nucleotide position 560, causing the aspartic acid (D) at amino acid position 187 to be replaced by a glycine (G). 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	0.31
BayesDel_addAF	Benign	-0.023	T
BayesDel_noAF	Benign	-0.27
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.055	T;T;.
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.94	D;D;D
M_CAP	Pathogenic	0.42	D
MetaRNN	Uncertain	0.53	D;D;D
MetaSVM	Benign	-0.67	T
MutationAssessor	Uncertain	2.8	.;M;M
PrimateAI	Uncertain	0.66	T
PROVEAN	Uncertain	-3.6	D;D;N
REVEL	Benign	0.28
Sift	Benign	0.14	T;T;T
Sift4G	Benign	0.27	T;T;T
Polyphen		0.99, 0.94	.;D;P
Vest4		0.60, 0.73
MVP		0.55
MPC		1.5
ClinPred		0.89	D
GERP RS		5.9
Varity_R		0.66
gMVP		0.71

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: chrX-107084455;