8-22067145-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001387751.1(DMTN):​c.79C>T​(p.Pro27Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000206 in 1,456,060 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

DMTN
NM_001387751.1 missense

Scores

6
9
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.70
Variant links:
Genes affected
DMTN (HGNC:3382): (dematin actin binding protein) The protein encoded by this gene is an actin binding and bundling protein that plays a structural role in erythrocytes, by stabilizing and attaching the spectrin/actin cytoskeleton to the erythrocyte membrane in a phosphorylation-dependent manner. This protein contains a core domain in the N-terminus, and a headpiece domain in the C-terminus that binds F-actin. When purified from erythrocytes, this protein exists as a trimer composed of two 48 kDa polypeptides and a 52 kDa polypeptide. The different subunits arise from alternative splicing in the 3' coding region, where the headpiece domain is located. Disruption of this gene has been correlated with the autosomal dominant Marie Unna hereditary hypotrichosis disease, while loss of heterozygosity of this gene is thought to play a role in prostate cancer progression. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DMTNNM_001387751.1 linkc.79C>T p.Pro27Ser missense_variant Exon 3 of 16 ENST00000358242.6 NP_001374680.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DMTNENST00000358242.6 linkc.79C>T p.Pro27Ser missense_variant Exon 3 of 16 5 NM_001387751.1 ENSP00000350977.3 Q08495-1

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
0.00000206
AC:
3
AN:
1456060
Hom.:
0
Cov.:
34
AF XY:
0.00000138
AC XY:
1
AN XY:
724504
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000259
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jan 16, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.79C>T (p.P27S) alteration is located in exon 3 (coding exon 2) of the DMTN gene. This alteration results from a C to T substitution at nucleotide position 79, causing the proline (P) at amino acid position 27 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.53
BayesDel_addAF
Uncertain
0.026
T
BayesDel_noAF
Benign
-0.20
CADD
Pathogenic
29
DANN
Pathogenic
1.0
DEOGEN2
Uncertain
0.47
.;.;T;.;T;T;.;T;T;.;.;.
Eigen
Pathogenic
0.69
Eigen_PC
Uncertain
0.65
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Uncertain
0.91
D;D;.;.;.;.;D;D;.;.;.;D
M_CAP
Benign
0.043
D
MetaRNN
Uncertain
0.60
D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Benign
-0.46
T
MutationAssessor
Pathogenic
3.3
.;M;M;.;M;M;.;M;M;M;M;.
PrimateAI
Uncertain
0.62
T
PROVEAN
Pathogenic
-6.7
D;D;D;D;D;D;D;D;D;D;D;.
REVEL
Uncertain
0.30
Sift
Pathogenic
0.0
D;D;D;D;D;D;D;D;D;D;D;.
Sift4G
Pathogenic
0.0
D;D;D;D;D;D;D;D;D;D;D;D
Polyphen
1.0, 1.0
.;D;D;.;D;D;.;D;D;D;D;.
Vest4
0.74, 0.74, 0.53, 0.54, 0.74, 0.74
MutPred
0.38
Gain of phosphorylation at P27 (P = 0.0132);Gain of phosphorylation at P27 (P = 0.0132);Gain of phosphorylation at P27 (P = 0.0132);Gain of phosphorylation at P27 (P = 0.0132);Gain of phosphorylation at P27 (P = 0.0132);Gain of phosphorylation at P27 (P = 0.0132);Gain of phosphorylation at P27 (P = 0.0132);Gain of phosphorylation at P27 (P = 0.0132);Gain of phosphorylation at P27 (P = 0.0132);Gain of phosphorylation at P27 (P = 0.0132);Gain of phosphorylation at P27 (P = 0.0132);Gain of phosphorylation at P27 (P = 0.0132);
MVP
0.61
MPC
1.0
ClinPred
1.0
D
GERP RS
5.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.75
gMVP
0.71

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-21924656; API