GeneBe

rs200951949

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001034850.3(RETREG1):​c.*65_*71delAAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000882 in 1,133,264 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 8.8e-7 ( 0 hom. )

Consequence

RETREG1
NM_001034850.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.982

Publications

0 publications found
Variant links:
Genes affected
RETREG1 (HGNC:25964): (reticulophagy regulator 1) The protein encoded by this gene is a cis-Golgi transmembrane protein that may be necessary for the long-term survival of nociceptive and autonomic ganglion neurons. Mutations in this gene are a cause of hereditary sensory and autonomic neuropathy type IIB (HSAN IIB), and this gene may also play a role in susceptibility to vascular dementia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]
RETREG1 Gene-Disease associations (from GenCC):
  • hereditary sensory and autonomic neuropathy
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • neuropathy, hereditary sensory and autonomic, type 2B
    Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
  • hereditary sensory and autonomic neuropathy type 2
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001034850.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
RETREG1
NM_001034850.3
MANE Select
c.*65_*71delAAAAAAA
3_prime_UTR
Exon 9 of 9NP_001030022.1Q9H6L5-1
RETREG1
NM_019000.5
c.*65_*71delAAAAAAA
3_prime_UTR
Exon 7 of 7NP_061873.2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
RETREG1
ENST00000306320.10
TSL:1 MANE Select
c.*65_*71delAAAAAAA
3_prime_UTR
Exon 9 of 9ENSP00000304642.9Q9H6L5-1
RETREG1
ENST00000399793.6
TSL:1
c.*65_*71delAAAAAAA
3_prime_UTR
Exon 7 of 7ENSP00000382691.2Q9H6L5-2
RETREG1
ENST00000510362.6
TSL:1
n.*65_*71delAAAAAAA
non_coding_transcript_exon
Exon 7 of 8ENSP00000425089.2H0Y9U4

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
8.82e-7
AC:
1
AN:
1133264
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
568544
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
24972
American (AMR)
AF:
0.00
AC:
0
AN:
26008
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20182
East Asian (EAS)
AF:
0.00
AC:
0
AN:
34312
South Asian (SAS)
AF:
0.00
AC:
0
AN:
63662
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
35868
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4554
European-Non Finnish (NFE)
AF:
0.00000114
AC:
1
AN:
875664
Other (OTH)
AF:
0.00
AC:
0
AN:
48042
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.98

Splicing

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

Publications

Other links and lift over

dbSNP: rs200951949; hg19: chr5-16474778; API