rs770561064
Variant names:
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
NM_002420.6 start_lost
Scores
3
14
Clinical Significance
Conservation
PhyloP100: 0.0580
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]
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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 |
---|---|---|---|---|---|---|---|---|
TRPM1 | NM_001252024.2 | c.69G>A | p.Met23Ile | missense_variant | Exon 3 of 28 | ENST00000256552.11 | NP_001238953.1 | |
TRPM1 | NM_002420.6 | c.3G>A | p.Met1? | start_lost | Exon 2 of 27 | NP_002411.3 | ||
TRPM1 | NM_001252030.2 | c.3G>A | p.Met1? | start_lost | Exon 2 of 3 | NP_001238959.1 | ||
TRPM1 | NM_001252020.2 | c.120G>A | p.Met40Ile | missense_variant | Exon 2 of 27 | NP_001238949.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152112Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000112 AC: 28AN: 249536Hom.: 0 AF XY: 0.0000960 AC XY: 13AN XY: 135390
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GnomAD4 exome AF: 0.0000604 AC: 88AN: 1456104Hom.: 0 Cov.: 27 AF XY: 0.0000648 AC XY: 47AN XY: 724860
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GnomAD4 genome AF: 0.0000789 AC: 12AN: 152112Hom.: 0 Cov.: 33 AF XY: 0.0000808 AC XY: 6AN XY: 74282
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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 submitter | research | Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.;.;T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;T;T;D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;T;T;D;D;D
MetaSVM
Benign
T
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;D;D;T;T;D
Sift4G
Benign
T;D;D;D;T;D
Polyphen
B;.;.;.;.;.
Vest4
MutPred
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
MPC
0.23
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at