rs138568411

Variant names:

• chr5-147650538-T-A
• rs138568411
• NM_001270941.2:c.637A>T

Your query was ambiguous. Multiple possible variants found:

• chr5-147650538-T-A
• chr5-147650538-T-C

Variant summary

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

The NM_001270941.2(JAKMIP2):​c.637A>T​(p.Ile213Phe) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: JAKMIP2 NM_001270941.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.73

Genes affected

JAKMIP2 (HGNC:29067): (janus kinase and microtubule interacting protein 2) The protein encoded by this gene is reported to be a component of the Golgi matrix. It may act as a golgin protein by negatively regulating transit of secretory cargo and by acting as a structural scaffold of the Golgi. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

JAKMIP2-AS1 (HGNC:27203): (JAKMIP2 antisense RNA 1)

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
JAKMIP2	NM_001270941.2	c.637A>T	p.Ile213Phe	missense_variant	Exon 4 of 22	ENST00000616793.5	NP_001257870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAKMIP2	ENST00000616793.5	c.637A>T	p.Ile213Phe	missense_variant	Exon 4 of 22	5	NM_001270941.2	ENSP00000479248.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.73
BayesDel_addAF	Uncertain	0.10	D
BayesDel_noAF	Benign	-0.090
CADD	Pathogenic	27
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.46	.;.;T;.
Eigen	Uncertain	0.67
Eigen_PC	Uncertain	0.65
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Pathogenic	0.98	D;D;D;D
M_CAP	Benign	0.015	T
MetaRNN	Uncertain	0.67	D;D;D;D
MetaSVM	Benign	-0.77	T
MutationAssessor	Uncertain	2.3	M;M;M;.
PrimateAI	Pathogenic	0.85	D
PROVEAN	Uncertain	-2.7	.;D;D;D
REVEL	Benign	0.21
Sift	Uncertain	0.0050	.;D;D;D
Sift4G	Uncertain	0.047	D;D;T;T
Polyphen		0.96	D;.;D;.
Vest4		0.85
MutPred		0.38		Loss of methylation at K216 (P = 0.072);Loss of methylation at K216 (P = 0.072);Loss of methylation at K216 (P = 0.072);.;
MVP		0.37
MPC		2.0
ClinPred		0.96	D
GERP RS		5.4
Varity_R		0.54
gMVP		0.77

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

LitVar

Other links and lift over

dbSNP: rs138568411; hg19: chr5-147030101;