17-46704759-G-A

Position:

• chr17-46704759-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP2 PP5

The NM_006178.4(NSF):​c.1375G>A​(p.Ala459Thr) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.

• Frequency: Genomes: not found (cov: 23)
• Consequence: NSF NM_006178.4 missense, splice_region
• Scores: Splicing: ADA: 0.9949
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 9.67

Genes affected

NSF (HGNC:8016): (N-ethylmaleimide sensitive factor, vesicle fusing ATPase) Enables PDZ domain binding activity and ionotropic glutamate receptor binding activity. Involved in intracellular protein transport; positive regulation of protein catabolic process; and positive regulation of receptor recycling. Located in Golgi apparatus; cytosol; and plasma membrane. Implicated in developmental and epileptic encephalopathy. [provided by Alliance of Genome Resources, Apr 2022]

LRRC37A2 (HGNC:32404): (leucine rich repeat containing 37 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

NSF (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), NSF. . Gene score misZ 2.584 (greater than the threshold 3.09). Trascript score misZ 3.1056 (greater than threshold 3.09). GenCC has associacion of gene with developmental and epileptic encephalopathy 96.
• PP5: Variant 17-46704759-G-A is Pathogenic according to our data. Variant chr17-46704759-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 1120201.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NSF	NM_006178.4	c.1375G>A	p.Ala459Thr	missense_variant, splice_region_variant	13/21	ENST00000398238.8	NP_006169.2
LRRC37A2	XM_024450773.2	c.4809+154240G>A		intron_variant			XP_024306541.1
NSF	NR_040116.2	n.1442G>A		splice_region_variant, non_coding_transcript_exon_variant	12/20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NSF	ENST00000398238.8	c.1375G>A	p.Ala459Thr	missense_variant, splice_region_variant	13/21	1	NM_006178.4	ENSP00000381293.4

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 23

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Developmental and epileptic encephalopathy 96 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

May 28, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.59
BayesDel_addAF	Uncertain	0.12	D
BayesDel_noAF	Uncertain	-0.060
CADD	Pathogenic	33
DANN	Uncertain	1.0
DEOGEN2	Benign	0.30	T;T
Eigen	Pathogenic	0.74
Eigen_PC	Pathogenic	0.73
FATHMM_MKL	Pathogenic	0.99	D
M_CAP	Benign	0.044	D
MetaRNN	Uncertain	0.62	D;D
MetaSVM	Benign	-0.53	T
MutationAssessor	Uncertain	2.1	M;.
PrimateAI	Uncertain	0.70	T
PROVEAN	Uncertain	-3.0	D;.
REVEL	Uncertain	0.31
Sift	Uncertain	0.013	D;.
Sift4G	Benign	0.23	T;T
Polyphen		0.99	D;.
Vest4		0.66
MutPred		0.35		Loss of helix (P = 0.0558);.;
MVP		0.73
MPC		2.6
ClinPred		0.98	D
GERP RS		5.0
Varity_R		0.31
gMVP		0.78

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.99
dbscSNV1_RF	Benign	0.69
SpliceAI score (max)		0.12		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: chr17-44782125;