rs137852685

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PM5PP3

The NM_004387.4(NKX2-5):​c.482G>T​(p.Arg161Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,451,422 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R161P) has been classified as Pathogenic.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

NKX2-5
NM_004387.4 missense

Scores

8
10
1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.12
Variant links:
Genes affected
NKX2-5 (HGNC:2488): (NK2 homeobox 5) This gene encodes a homeobox-containing transcription factor. This transcription factor functions in heart formation and development. Mutations in this gene cause atrial septal defect with atrioventricular conduction defect, and also tetralogy of Fallot, which are both heart malformation diseases. Mutations in this gene can also cause congenital hypothyroidism non-goitrous type 5, a non-autoimmune condition. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

PM1
In a DNA_binding_region Homeobox (size 59) in uniprot entity NKX25_HUMAN there are 47 pathogenic changes around while only 0 benign (100%) in NM_004387.4
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr5-173233062-C-G is described in Lovd as [Pathogenic].
PP3
MetaRNN computational evidence supports a deleterious effect, 0.773

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NKX2-5NM_004387.4 linkc.482G>T p.Arg161Leu missense_variant Exon 2 of 2 ENST00000329198.5 NP_004378.1 P52952-1A0A0S2Z383
NKX2-5NM_001166176.2 linkc.*281G>T 3_prime_UTR_variant Exon 2 of 2 NP_001159648.1 P52952-2
NKX2-5NM_001166175.2 linkc.*435G>T 3_prime_UTR_variant Exon 2 of 2 NP_001159647.1 P52952-3A0A0S2Z3K2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NKX2-5ENST00000329198.5 linkc.482G>T p.Arg161Leu missense_variant Exon 2 of 2 1 NM_004387.4 ENSP00000327758.4 P52952-1
NKX2-5ENST00000424406 linkc.*435G>T 3_prime_UTR_variant Exon 2 of 2 1 ENSP00000395378.2 P52952-3
NKX2-5ENST00000521848 linkc.*281G>T 3_prime_UTR_variant Exon 2 of 2 2 ENSP00000427906.1 P52952-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.89e-7
AC:
1
AN:
1451422
Hom.:
0
Cov.:
35
AF XY:
0.00
AC XY:
0
AN XY:
721346
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.03e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.98
BayesDel_addAF
Pathogenic
0.19
D
BayesDel_noAF
Uncertain
0.030
CADD
Pathogenic
31
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.97
D
Eigen
Uncertain
0.45
Eigen_PC
Uncertain
0.41
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Uncertain
0.96
D
M_CAP
Pathogenic
0.58
D
MetaRNN
Pathogenic
0.77
D
MetaSVM
Pathogenic
0.97
D
MutationAssessor
Uncertain
2.7
M
PrimateAI
Uncertain
0.79
T
PROVEAN
Pathogenic
-6.3
D
REVEL
Pathogenic
0.66
Sift
Uncertain
0.0020
D
Sift4G
Uncertain
0.0040
D
Polyphen
0.59
P
Vest4
0.48
MutPred
0.68
Loss of MoRF binding (P = 0.0266);
MVP
0.92
MPC
1.5
ClinPred
0.98
D
GERP RS
3.2
Varity_R
0.88
gMVP
0.46

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: chr5-172660065; API