7-36357416-T-A

Variant names:

• chr7-36357416-T-A
• rs369837787
• NM_001199706.2:c.200A>T

Variant summary

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

The NM_001199706.2(MATCAP2):​c.200A>T​(p.Lys67Ile) 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. 14/21 in silico tools predict 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. K67T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MATCAP2 NM_001199706.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 0 publications found

Genes affected

MATCAP2 (HGNC:22206): (microtubule associated tyrosine carboxypeptidase 2)

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=0.14929843).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199706.2. 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
	MATCAP2	NM_001199706.2	MANE Select	c.200A>T	p.Lys67Ile	missense	Exon 2 of 7	NP_001186635.1	Q8NCT3-6
	MATCAP2	NM_001100425.2		c.353A>T	p.Lys118Ile	missense	Exon 3 of 7	NP_001093895.1	Q8NCT3-1
	MATCAP2	NM_001199707.2		c.314A>T	p.Lys105Ile	missense	Exon 2 of 6	NP_001186636.1	Q8NCT3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MATCAP2	ENST00000440378.6	TSL:1 MANE Select	c.200A>T	p.Lys67Ile	missense	Exon 2 of 7	ENSP00000390837.1	Q8NCT3-6
	MATCAP2	ENST00000297063.10	TSL:1	c.353A>T	p.Lys118Ile	missense	Exon 3 of 7	ENSP00000297063.6	Q8NCT3-1
	MATCAP2	ENST00000338533.9	TSL:1	c.314A>T	p.Lys105Ile	missense	Exon 2 of 6	ENSP00000344805.5	Q8NCT3-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
BayesDel_addAF	Benign	-0.028	T
BayesDel_noAF	Benign	-0.28
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Benign	0.070	T
Eigen	Benign	0.087
Eigen_PC	Benign	0.022
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.87	D
M_CAP	Benign	0.024	T
MetaRNN	Benign	0.15	T
MetaSVM	Benign	-0.62	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		1.4
PrimateAI	Benign	0.33	T
PROVEAN	Benign	-1.8	N
REVEL	Benign	0.10
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.0030	D
Polyphen		0.95	P
Vest4		0.33
MutPred		0.24		Loss of methylation at K118 (P = 0.0022)
MVP		0.34
MPC		1.2
ClinPred		0.91	D
GERP RS		-2.0
Varity_R		0.15
gMVP		0.31
Mutation Taster		=65/35	polymorphism

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

Other links and lift over

dbSNP: rs369837787; hg19: chr7-36397025;