17-81559372-C-G

Variant names:

• chr17-81559372-C-G
• rs761777816
• NM_017921.4:c.1714G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_017921.4(NPLOC4):​c.1714G>C​(p.Val572Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V572A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: NPLOC4 NM_017921.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483
• Publications: 0 publications found

Genes affected

NPLOC4 (HGNC:18261): (NPL4 homolog, ubiquitin recognition factor) Predicted to enable ATPase binding activity; ubiquitin binding activity; and ubiquitin protein ligase binding activity. Predicted to contribute to K48-linked polyubiquitin modification-dependent protein binding activity and K63-linked polyubiquitin modification-dependent protein binding activity. Involved in negative regulation of RIG-I signaling pathway; negative regulation of type I interferon production; and proteolysis involved in cellular protein catabolic process. Located in nucleus. Part of UFD1-NPL4 complex and VCP-NPL4-UFD1 AAA ATPase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.0617823).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017921.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPLOC4	NM_017921.4	MANE Select	c.1714G>C	p.Val572Leu	missense	Exon 17 of 17	NP_060391.2	Q8TAT6-1
	NPLOC4	NM_001369698.1		c.1729G>C	p.Val577Leu	missense	Exon 17 of 17	NP_001356627.1
	NPLOC4	NM_001438810.1		c.1773G>C	p.Pro591Pro	synonymous	Exon 18 of 18	NP_001425739.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPLOC4	ENST00000331134.11	TSL:1 MANE Select	c.1714G>C	p.Val572Leu	missense	Exon 17 of 17	ENSP00000331487.5	Q8TAT6-1
	NPLOC4	ENST00000573519.5	TSL:1	c.372G>C	p.Pro124Pro	synonymous	Exon 5 of 5	ENSP00000459457.1	I3L281
	NPLOC4	ENST00000572760.5	TSL:1	c.108G>C	p.Pro36Pro	synonymous	Exon 3 of 3	ENSP00000467400.1	K7EJN1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.080
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	7.7
DANN	Benign	0.67
DEOGEN2	Benign	0.033	T
Eigen	Benign	-0.83
Eigen_PC	Benign	-0.73
FATHMM_MKL	Benign	0.72	D
LIST_S2	Benign	0.82	T
M_CAP	Benign	0.0049	T
MetaRNN	Benign	0.062	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.1	L
PhyloP100		0.48
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-1.0	N
REVEL	Benign	0.035
Sift	Benign	0.25	T
Sift4G	Benign	0.65	T
Polyphen		0.0	B
Vest4		0.060
MutPred		0.22		Loss of catalytic residue at V572 (P = 0.0543)
MVP		0.16
MPC		0.013
ClinPred		0.068	T
GERP RS		2.9
Varity_R		0.056
gMVP		0.15

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs761777816; hg19: chr17-79526398;