GeneBe

rs531550505

Positions:

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2

The NM_144599.5(NIPA1):​c.27_47del​(p.Ala10_Ala16del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000448 in 1,071,500 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000034 ( 0 hom., cov: 6)
Exomes 𝑓: 0.000046 ( 3 hom. )

Consequence

NIPA1
NM_144599.5 inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.48
Variant links:
Genes affected
NIPA1 (HGNC:17043): (NIPA magnesium transporter 1) This gene encodes a magnesium transporter that associates with early endosomes and the cell surface in a variety of neuronal and epithelial cells. This protein may play a role in nervous system development and maintenance. Multiple transcript variants encoding different isoforms have been found for this gene. Mutations in this gene have been associated with autosomal dominant spastic paraplegia 6. [provided by RefSeq, Nov 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_144599.5
BS2
High AC in GnomAd4 at 5 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NIPA1NM_144599.5 linkuse as main transcriptc.27_47del p.Ala10_Ala16del inframe_deletion 1/5 ENST00000337435.9 NP_653200.2
NIPA1NM_001142275.1 linkuse as main transcriptc.-48+435_-48+455del intron_variant NP_001135747.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NIPA1ENST00000337435.9 linkuse as main transcriptc.27_47del p.Ala10_Ala16del inframe_deletion 1/51 NM_144599.5 ENSP00000337452 P1Q7RTP0-1
NIPA1ENST00000437912.6 linkuse as main transcriptc.-48+12370_-48+12390del intron_variant 1 ENSP00000393962 Q7RTP0-2
NIPA1ENST00000561183.5 linkuse as main transcriptc.-48+435_-48+455del intron_variant 1 ENSP00000453722 Q7RTP0-2
NIPA1ENST00000560069.5 linkuse as main transcriptn.31+435_31+455del intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.0000344
AC:
5
AN:
145406
Hom.:
0
Cov.:
6
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000207
Gnomad SAS
AF:
0.000638
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000153
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000347
AC:
7
AN:
20176
Hom.:
1
AF XY:
0.000474
AC XY:
6
AN XY:
12652
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00128
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000114
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000464
AC:
43
AN:
926094
Hom.:
3
AF XY:
0.0000723
AC XY:
32
AN XY:
442826
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000171
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00110
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000207
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000344
AC:
5
AN:
145406
Hom.:
0
Cov.:
6
AF XY:
0.0000424
AC XY:
3
AN XY:
70686
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000207
Gnomad4 SAS
AF:
0.000638
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000153
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs531550505; hg19: chr15-23086391; API