rs200530055

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2PP5_Very_Strong

The NM_001383.6(DPH1):​c.359T>C​(p.Leu120Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000496 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).

Frequency

Genomes: 𝑓 0.00029 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00052 ( 0 hom. )

Consequence

DPH1
NM_001383.6 missense

Scores

12
6
1

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:9

Conservation

PhyloP100: 6.00
Variant links:
Genes affected
DPH1 (HGNC:3003): (diphthamide biosynthesis 1) The protein encoded by this gene is an enzyme involved in the biosynthesis of diphthamide, a modified histidine found only in elongation factor-2 (EEF2). Diphthamide residues in EEF2 are targeted for ADP-ribosylation by diphtheria toxin and Pseudomonas exotoxin A. Defects in this gene have been associated with both ovarian cancer and autosomal recessive intellectual disability with short stature, craniofacial, and ectodermal anomalies. [provided by RefSeq, Oct 2016]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 10 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-2036050-T-C is Pathogenic according to our data. Variant chr17-2036050-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 521028.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-2036050-T-C is described in Lovd as [Pathogenic]. Variant chr17-2036050-T-C is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DPH1NM_001383.6 linkc.359T>C p.Leu120Pro missense_variant Exon 4 of 13 ENST00000263083.12 NP_001374.4 Q9BZG8-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DPH1ENST00000263083.12 linkc.359T>C p.Leu120Pro missense_variant Exon 4 of 13 1 NM_001383.6 ENSP00000263083.7 Q9BZG8-4

Frequencies

GnomAD3 genomes
AF:
0.000289
AC:
44
AN:
152124
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000145
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000786
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000323
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.000289
AC:
72
AN:
248874
Hom.:
0
AF XY:
0.000333
AC XY:
45
AN XY:
135294
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000609
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000464
Gnomad NFE exome
AF:
0.000426
Gnomad OTH exome
AF:
0.000331
GnomAD4 exome
AF:
0.000517
AC:
756
AN:
1461728
Hom.:
0
Cov.:
31
AF XY:
0.000495
AC XY:
360
AN XY:
727186
show subpopulations
Gnomad4 AFR exome
AF:
0.000149
Gnomad4 AMR exome
AF:
0.000761
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000375
Gnomad4 NFE exome
AF:
0.000614
Gnomad4 OTH exome
AF:
0.000530
GnomAD4 genome
AF:
0.000289
AC:
44
AN:
152242
Hom.:
0
Cov.:
32
AF XY:
0.000255
AC XY:
19
AN XY:
74434
show subpopulations
Gnomad4 AFR
AF:
0.000144
Gnomad4 AMR
AF:
0.000785
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000324
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.000385
Hom.:
0
Bravo
AF:
0.000382
TwinsUK
AF:
0.00135
AC:
5
ALSPAC
AF:
0.000519
AC:
2
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000235
AC:
2
ExAC
AF:
0.000239
AC:
29
EpiCase
AF:
0.000818
EpiControl
AF:
0.000948

ClinVar

Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:9
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Developmental delay with short stature, dysmorphic facial features, and sparse hair Pathogenic:4
Likely pathogenic, criteria provided, single submitterclinical testingCentre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille-- -
Likely pathogenic, criteria provided, single submitterclinical testingEquipe Genetique des Anomalies du Developpement, Université de BourgogneAug 05, 2016- -
Pathogenic, criteria provided, single submitterclinical testing3billion, Medical GeneticsMay 22, 2022The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.029%). Missense changes are a common disease-causing mechanism. Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 30877278). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.73; 3Cnet: 3CNET). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000521028). The variant has been reported to co-segregate with the disease in at least one similarly affected relative/individual in the same family or similarly affected unrelated family (PMID: 30877278). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
Likely pathogenic, criteria provided, single submitterclinical testingGreenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic CenterMar 11, 2022PS3, PM3 -
Developmental delay with short stature, dysmorphic facial features, and sparse hair 1 Pathogenic:2
Pathogenic, no assertion criteria providedliterature onlyOMIMSep 30, 2022- -
Likely pathogenic, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpMar 13, 2024Variant summary: DPH1 c.359T>C (p.Leu120Pro) results in a non-conservative amino acid change in the encoded protein sequence. Three of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00029 in 248874 control chromosomes. This frequency does not allow conclusion about variant significance. c.359T>C has been reported in the literature in 2 homozygous siblings affected with Developmental Delay With Short Stature, Dysmorphic Facial Features, And Sparse Hair 1 (Lefebvre_2021, Urreizti_2020) . These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function demonstrating reduced amounts of ADP-ribosylated eEF2 (Urreizti_2020). The following publications have been ascertained in the context of this evaluation (PMID: 32732226, 30877278). ClinVar contains an entry for this variant (Variation ID: 521028). Based on the evidence outlined above, the variant was classified as likely pathogenic. -
Inborn genetic diseases Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsNov 14, 2024The c.374T>C (p.L125P) alteration is located in coding exon 4 of the DPH1 gene. This alteration results from a T to C substitution at nucleotide position 374, causing the leucine (L) at amino acid position 125 to be replaced by a proline (P). Based on data from gnomAD, the C allele has an overall frequency of 0.029% (80/280222) total alleles studied. The highest observed frequency was 0.059% (21/35334) of Latino alleles. This variant has been identified in the homozygous state and/or in conjunction with other DPH1 variant(s) in individual(s) with features consistent with DPH1-related neurodevelopmental disorder (Ambry internal data; Urreizti, 2020; Lefebvre, 2021; Faas, 2023; Drexler, 2023). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic. -
DPH1-related disorder Pathogenic:1
Likely pathogenic, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesJan 23, 2024The DPH1 c.374T>C variant is predicted to result in the amino acid substitution p.Leu125Pro. This variant in the homozygous state has been reported in a neonatal patient who was diagnosed with structural anomalies such as birth defects, dysmorphic features, cardiac, craniofacial, and skeletal defects (Powis et al. 2018. PubMed ID: 29565416, Supplementary Table 1). This variant was also reported in the homozygous state in two siblings presenting with a variety of features including developmental delay, central nervous system malformations, short stature, unusual skull shape, and genital anomalies (Urreizti et al. 2020. PubMed ID: 30877278), and a fetus with multiple congenital abnormalities (Lefebvre et al. 2021. PubMed ID: 32732226). Functional studies of DPH1 p.Leu125Pro showed reduced enzyme activity (Urreizti et al. 2020. PubMed ID: 30877278). This variant is reported in 0.059% of alleles in individuals of Latino descent in gnomAD. This variant is interpreted as likely pathogenic. -
not provided Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingGeneDxJul 22, 2024Published functional studies demonstrate a damaging effect of reduced ADP-ribosylated eEF2 (PMID: 30877278); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26220823, 25558065, 29565416, 24895408, 14744934, 30877278, 32732226, 34297361, 27460824, 26415585, 33704902, 37675463, 36647814, 37326029) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.95
BayesDel_addAF
Uncertain
0.025
T
BayesDel_noAF
Pathogenic
0.22
CADD
Pathogenic
30
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.64
D;.
Eigen
Pathogenic
0.84
Eigen_PC
Pathogenic
0.76
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Pathogenic
0.98
D;D
M_CAP
Uncertain
0.18
D
MetaRNN
Uncertain
0.73
D;D
MetaSVM
Uncertain
-0.11
T
MutationAssessor
Pathogenic
3.5
H;.
PrimateAI
Pathogenic
0.87
D
PROVEAN
Pathogenic
-6.8
D;.
REVEL
Pathogenic
0.73
Sift
Pathogenic
0.0
D;.
Sift4G
Pathogenic
0.0
D;D
Polyphen
1.0
D;.
Vest4
0.97
MVP
0.82
MPC
0.75
ClinPred
0.48
T
GERP RS
5.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.97
gMVP
0.95

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs200530055; hg19: chr17-1939344; API