rs770561064

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_ModeratePM2PP5_Moderate

The NM_002420.6(TRPM1):​c.3G>A​(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000622 in 1,608,216 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★).

Frequency

Genomes: 𝑓 0.000079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000060 ( 0 hom. )

Consequence

TRPM1
NM_002420.6 start_lost

Scores

3
14

Clinical Significance

Likely pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 0.0580
Variant links:
Genes affected
TRPM1 (HGNC:7146): (transient receptor potential cation channel subfamily M member 1) This gene encodes a member of the transient receptor potential melastatin subfamily of transient receptor potential ion channels. The encoded protein is a calcium permeable cation channel that is expressed in melanocytes and may play a role in melanin synthesis. Specific mutations in this gene are the cause autosomal recessive complete congenital stationary night blindness-1C. The expression of this protein is inversely correlated with melanoma aggressiveness and as such it is used as a prognostic marker for melanoma metastasis. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PVS1
Start lost variant, next in-frame start position is after 3 pathogenic variants. Next in-frame start position is after 210 CDS bases. Genomic position: 31070034. Lost 0.044 part of the original CDS.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 15-31076919-C-T is Pathogenic according to our data. Variant chr15-31076919-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 191053.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRPM1NM_001252024.2 linkc.69G>A p.Met23Ile missense_variant Exon 3 of 28 ENST00000256552.11 NP_001238953.1 Q7Z4N2-6
TRPM1NM_002420.6 linkc.3G>A p.Met1? start_lost Exon 2 of 27 NP_002411.3 Q7Z4N2-1
TRPM1NM_001252030.2 linkc.3G>A p.Met1? start_lost Exon 2 of 3 NP_001238959.1 Q7Z4N2-7
TRPM1NM_001252020.2 linkc.120G>A p.Met40Ile missense_variant Exon 2 of 27 NP_001238949.1 Q7Z4N2-5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRPM1ENST00000256552.11 linkc.69G>A p.Met23Ile missense_variant Exon 3 of 28 1 NM_001252024.2 ENSP00000256552.7 Q7Z4N2-6

Frequencies

GnomAD3 genomes
AF:
0.0000789
AC:
12
AN:
152112
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000966
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000393
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000112
AC:
28
AN:
249536
Hom.:
0
AF XY:
0.0000960
AC XY:
13
AN XY:
135390
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000521
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000556
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000795
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000604
AC:
88
AN:
1456104
Hom.:
0
Cov.:
27
AF XY:
0.0000648
AC XY:
47
AN XY:
724860
show subpopulations
Gnomad4 AFR exome
AF:
0.000540
Gnomad4 AMR exome
AF:
0.000470
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000343
Gnomad4 OTH exome
AF:
0.000133
GnomAD4 genome
AF:
0.0000789
AC:
12
AN:
152112
Hom.:
0
Cov.:
33
AF XY:
0.0000808
AC XY:
6
AN XY:
74282
show subpopulations
Gnomad4 AFR
AF:
0.0000966
Gnomad4 AMR
AF:
0.000393
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000478
Alfa
AF:
0.000169
Hom.:
0
Bravo
AF:
0.000106
ExAC
AF:
0.0000497
AC:
6
EpiCase
AF:
0.0000545
EpiControl
AF:
0.000119

ClinVar

Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitterresearchGenomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.53
T
BayesDel_noAF
Benign
-0.66
CADD
Benign
0.23
DANN
Benign
0.85
DEOGEN2
Benign
0.073
T;.;.;T;T;.
Eigen
Benign
-1.8
Eigen_PC
Benign
-1.9
FATHMM_MKL
Benign
0.055
N
LIST_S2
Uncertain
0.90
D;T;T;D;D;D
M_CAP
Benign
0.010
T
MetaRNN
Uncertain
0.52
D;T;T;D;D;D
MetaSVM
Benign
-1.1
T
PrimateAI
Uncertain
0.50
T
PROVEAN
Benign
-0.27
N;N;N;N;N;N
REVEL
Benign
0.18
Sift
Benign
0.27
T;D;D;T;T;D
Sift4G
Benign
0.37
T;D;D;D;T;D
Polyphen
0.0010
B;.;.;.;.;.
Vest4
0.074
MutPred
0.94
Gain of methylation at K2 (P = 0.0305);.;.;Gain of methylation at K2 (P = 0.0305);Gain of methylation at K2 (P = 0.0305);Gain of methylation at K2 (P = 0.0305);
MVP
0.22
MPC
0.23
ClinPred
0.48
T
GERP RS
-11
Varity_R
0.097
gMVP
0.14

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.12
Details are displayed if max score is > 0.2

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: rs770561064; hg19: chr15-31369122; COSMIC: COSV56641594; API