JAKMIP2

protein-coding

janus kinase and microtubule interacting protein 2

Gene summary

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]

MANE transcript

NM_001270941.2

Inheritance

—

ClinVar variants

U:64

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr5:147,585,438-147,782,775

External References & Databases

Ensembl (ENSG00000176049)

Transcript & Mutation Effects

hg38 • Region Span ~197.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to JAKMIP2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 55

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001270941.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			59 clinvar			59
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	64	0	0	64

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001270941.2	RefSeq	NP_001257870.1	20	MANE Select
ENST00000616793.5	Ensembl	ENSP00000479248.1	20	MANE Select
NM_001270934.2	RefSeq	NP_001257863.1	19	Standard
NM_001282282.2	RefSeq	NP_001269211.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
microtubule binding
kinase binding

Cellular Component

Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265272
Coding exons: 20
Length: 194349
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125732
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.36	236	433	0.545	0.0000247	5361
Missense (PolyPhen)		95	204.78	0.46391		2661
Synonymous	-0.264	165	161	1.03	0.00000926	1447
Loss of Function	6.16	4	51.9	0.0770	0.00000282	609

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.125

Intolerance Scores

LoFtool: 0.122
RVIS EVS: -1.2
RVIS percentile EVS: 5.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.806

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium