NM_001930.4(DHPS):c.912_917del (p.Tyr305_Ile306del) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 1, 2018
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000754488.1

Allele description [Variation Report for NM_001930.4(DHPS):c.912_917del (p.Tyr305_Ile306del)]

NM_001930.4(DHPS):c.912_917del (p.Tyr305_Ile306del)

Gene:

DHPS:deoxyhypusine synthase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

19p13.13

Genomic location:

Preferred name:

NM_001930.4(DHPS):c.912_917del (p.Tyr305_Ile306del)

HGVS:

NC_000019.10:g.12676115_12676120del
NG_015814.1:g.14312_14317del
NM_001206974.2:c.786_791del
NM_001369691.1:c.889-41_889-36del
NM_001369692.1:c.785-243_785-238del
NM_001369693.1:c.363_368del
NM_001930.4:c.912_917delMANE SELECT
NM_013406.3:c.785-14_785-9del
NP_001193903.1:p.Tyr263_Ile264del
NP_001356622.1:p.Tyr122_Ile123del
NP_001921.1:p.Tyr305_Ile306del
NC_000019.9:g.12786929_12786934del
NM_001930.3:c.912_917del6
NM_001930.3:c.912_917delTTACAT
NR_038192.2:n.922_927del
NR_161467.1:n.939_944del
NR_161468.1:n.1026_1031del
NR_161469.1:n.1006_1011del

Links:

OMIM: 600944.0003; dbSNP: rs1568317152

NCBI 1000 Genomes Browser:

rs1568317152

Molecular consequence:

NM_001206974.2:c.786_791del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001369693.1:c.363_368del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001930.4:c.912_917del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001369691.1:c.889-41_889-36del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369692.1:c.785-243_785-238del - intron variant - [Sequence Ontology: SO:0001627]
NM_013406.3:c.785-14_785-9del - intron variant - [Sequence Ontology: SO:0001627]
NR_038192.2:n.922_927del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_161467.1:n.939_944del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_161468.1:n.1026_1031del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_161469.1:n.1006_1011del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000804206	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Aug 1, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000804206

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Aug 1, 2018)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Recessive Rare Variants in Deoxyhypusine Synthase, an Enzyme Involved in the Synthesis of Hypusine, Are Associated with a Neurodevelopmental Disorder.

Ganapathi M, Padgett LR, Yamada K, Devinsky O, Willaert R, Person R, Au PB, Tagoe J, McDonald M, Karlowicz D, Wolf B, Lee J, Shen Y, Okur V, Deng L, LeDuc CA, Wang J, Hanner A, Mirmira RG, Park MH, Mastracci TL, Chung WK.

Am J Hum Genet. 2019 Feb 7;104(2):287-298. doi: 10.1016/j.ajhg.2018.12.017. Epub 2019 Jan 17.

PubMed [citation]

PMID:: 30661771
PMCID:: PMC6369575

Details of each submission

From GeneDx, SCV000804206.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The c.912_917delTTACAT variant in the DHPS gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The c.912_917delTTACAT variant causes an in-frame deletion of two amino acids, Tyrosine 305 and Isoleucine 306, denoted p.Tyr305_Ile306del. The Y305 residue is not conserved, and for the I306 residue, amino acids with similar properties to Isoleucine are tolerated across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. The c.912_917delTTACAT variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.912_917delTTACAT as a variant of uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 10, 2024

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