19-3193404-C-T

Variant names:

• chr19-3193404-C-T
• rs1057519322
• NM_020170.4:c.496C>T

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PP5

The NM_020170.4(NCLN):​c.496C>T​(p.Gln166*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NCLN NM_020170.4 stop_gained
• Clinical Significance: Likely pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 7.46
• Publications: 3 publications found

Genes affected

NCLN (HGNC:26923): (nicalin) Enables ribosome binding activity. Involved in protein stabilization; regulation of protein complex stability; and regulation of protein-containing complex assembly. Located in endoplasmic reticulum membrane. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 19-3193404-C-T is Pathogenic according to our data. Variant chr19-3193404-C-T is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 375276.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020170.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCLN	NM_020170.4	MANE Select	c.496C>T	p.Gln166*	stop_gained	Exon 3 of 15	NP_064555.2
	NCLN	NM_001321463.2		c.496C>T	p.Gln166*	stop_gained	Exon 3 of 15	NP_001308392.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCLN	ENST00000246117.9	TSL:1 MANE Select	c.496C>T	p.Gln166*	stop_gained	Exon 3 of 15	ENSP00000246117.3
	NCLN	ENST00000590671.5	TSL:2	c.274C>T	p.Gln92*	stop_gained	Exon 3 of 15	ENSP00000466678.1
	NCLN	ENST00000588428.5	TSL:5	c.185-2779C>T		intron	N/A	ENSP00000467011.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Hirschsprung disease, susceptibility to, 1 Pathogenic:1

Sep 26, 2016

Centre for Genomic Sciences, University of Hong Kong

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: in vivo

Nonsense mutation

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.62	D
BayesDel_noAF	Pathogenic	0.55
CADD	Pathogenic	41
DANN	Uncertain	1.0
Eigen	Pathogenic	0.79
Eigen_PC	Uncertain	0.62
FATHMM_MKL	Uncertain	0.93	D
PhyloP100		7.5
Vest4		0.40
GERP RS		4.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=6/194	disease causing (ClinVar)

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: rs1057519322; hg19: chr19-3193402; COSMIC: COSV55743233;