NM_001370259.2:c.*560G>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001370259.2(MEN1):c.*560G>T variant causes a 3 prime UTR 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MEN1
NM_001370259.2 3_prime_UTR
NM_001370259.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.78
Publications
0 publications found
Genes affected
MEN1 (HGNC:7010): (menin 1) This gene encodes menin, a tumor suppressor associated with a syndrome known as multiple endocrine neoplasia type 1. Menin is a scaffold protein that functions in histone modification and epigenetic gene regulation. It is thought to regulate several pathways and processes by altering chromatin structure through the modification of histones. [provided by RefSeq, May 2019]
MEN1 Gene-Disease associations (from GenCC):
- multiple endocrine neoplasia type 1Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics
- familial isolated hyperparathyroidismInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- pituitary gigantismInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- hereditary pheochromocytoma-paragangliomaInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Classification was made for transcript
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 (BayesDel_noAF=-0.77).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001370259.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MEN1 | TSL:5 MANE Select | c.*560G>T | 3_prime_UTR | Exon 10 of 10 | ENSP00000394933.3 | O00255-2 | |||
| MEN1 | TSL:1 | c.*560G>T | 3_prime_UTR | Exon 10 of 10 | ENSP00000308975.6 | O00255-2 | |||
| MEN1 | TSL:1 | c.*560G>T | 3_prime_UTR | Exon 11 of 11 | ENSP00000388016.2 | O00255-2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 90046Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 42252
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
90046
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
42252
African (AFR)
AF:
AC:
0
AN:
3922
American (AMR)
AF:
AC:
0
AN:
4250
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
5170
East Asian (EAS)
AF:
AC:
0
AN:
11742
South Asian (SAS)
AF:
AC:
0
AN:
2330
European-Finnish (FIN)
AF:
AC:
0
AN:
556
Middle Eastern (MID)
AF:
AC:
0
AN:
504
European-Non Finnish (NFE)
AF:
AC:
0
AN:
54532
Other (OTH)
AF:
AC:
0
AN:
7040
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Hyperparathyroidism (1)
-
1
-
Multiple endocrine neoplasia (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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