4-6054100-C-G

Position:

• chr4-6054100-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP5_Moderate

The NM_001099433.2(JAKMIP1):​c.1756G>C​(p.Asp586His) 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 Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. D586D) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: JAKMIP1 NM_001099433.2 missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 7.51

Genes affected

JAKMIP1 (HGNC:26460): (janus kinase and microtubule interacting protein 1) Enables GABA receptor binding activity and RNA binding activity. Involved in cognition. Is extrinsic component of membrane. Part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Apr 2022]

C4orf50 (HGNC:33766): (chromosome 4 open reading frame 50)

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 4-6054100-C-G is Pathogenic according to our data. Variant chr4-6054100-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 254206.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAKMIP1	NM_001099433.2	c.1756G>C	p.Asp586His	missense_variant	13/21	ENST00000409021.9
JAKMIP1	NM_001306133.2	c.1756G>C	p.Asp586His	missense_variant	13/13
JAKMIP1	NM_144720.4	c.1756G>C	p.Asp586His	missense_variant	13/13
JAKMIP1	NM_001306134.2	c.1261G>C	p.Asp421His	missense_variant	12/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAKMIP1	ENST00000409021.9	c.1756G>C	p.Asp586His	missense_variant	13/21	1	NM_001099433.2	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Smith-Magenis Syndrome-like Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine

Aug 15, 2016

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.95
BayesDel_addAF	Uncertain	0.033	T
BayesDel_noAF	Benign	-0.19
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Benign	0.33	T;.;.;T;T;.
Eigen	Pathogenic	0.84
Eigen_PC	Pathogenic	0.81
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.99	D;D;D;.;D;D
M_CAP	Benign	0.012	T
MetaRNN	Uncertain	0.46	T;T;T;T;T;T
MetaSVM	Benign	-0.36	T
MutationAssessor	Benign	2.0	.;M;.;M;M;.
MutationTaster	Benign	1.0	D;D;D;D;D
PrimateAI	Uncertain	0.72	T
PROVEAN	Pathogenic	-5.5	.;D;D;D;D;D
REVEL	Uncertain	0.30
Sift	Uncertain	0.0010	.;D;D;D;D;D
Sift4G	Uncertain	0.016	.;D;D;D;D;D
Polyphen		1.0	.;D;D;D;D;.
Vest4		0.77, 0.75, 0.75, 0.73
MutPred		0.12		.;Loss of helix (P = 0.2022);.;Loss of helix (P = 0.2022);Loss of helix (P = 0.2022);.;
MVP		0.46
MPC		1.8
ClinPred		0.99	D
GERP RS		5.5
Varity_R		0.78
gMVP		0.61

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: rs1114167350; hg19: chr4-6055827;