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NM_016077.5(PTRH2):c.254A>C (p.Gln85Pro) AND Neurologic, endocrine, and pancreatic disease, multisystem, infantile-onset 1

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Mar 17, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001799627.8

Allele description [Variation Report for NM_016077.5(PTRH2):c.254A>C (p.Gln85Pro)]

NM_016077.5(PTRH2):c.254A>C (p.Gln85Pro)

Gene:
PTRH2:peptidyl-tRNA hydrolase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q23.1
Genomic location:
Preferred name:
NM_016077.5(PTRH2):c.254A>C (p.Gln85Pro)
HGVS:
  • NC_000017.11:g.59697725T>G
  • NG_042064.1:g.14874A>C
  • NG_047043.1:g.83037T>G
  • NM_001015509.3:c.257A>C
  • NM_016077.5:c.254A>CMANE SELECT
  • NP_001015509.1:p.Gln86Pro
  • NP_001015509.1:p.Gln86Pro
  • NP_057161.1:p.Gln85Pro
  • NP_057161.1:p.Gln85Pro
  • NC_000017.10:g.57775086T>G
  • NM_001015509.2:c.257A>C
  • NM_016077.3:c.254A>C
  • NM_016077.4:c.254A>C
  • Q9Y3E5:p.Gln85Pro
Protein change:
Q85P; GLN85PRO
Links:
UniProtKB: Q9Y3E5#VAR_073386; OMIM: 608625.0002; dbSNP: rs730882234
NCBI 1000 Genomes Browser:
rs730882234
Molecular consequence:
  • NM_001015509.3:c.257A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_016077.5:c.254A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Neurologic, endocrine, and pancreatic disease, multisystem, infantile-onset 1 (IMNEPD1)
Identifiers:
MONDO: MONDO:8000012; MedGen: C4015728; Orphanet: 456312; OMIM: 616263

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000212240OMIM
no assertion criteria provided
Pathogenic
(Jan 13, 2015)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV002019564Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Nov 19, 2020)
germlineclinical testing

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

SCV004804830Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 17, 2024)
germlineresearch

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, research
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families.

Alazami AM, Patel N, Shamseldin HE, Anazi S, Al-Dosari MS, Alzahrani F, Hijazi H, Alshammari M, Aldahmesh MA, Salih MA, Faqeih E, Alhashem A, Bashiri FA, Al-Owain M, Kentab AY, Sogaty S, Al Tala S, Temsah MH, Tulbah M, Aljelaify RF, Alshahwan SA, Seidahmed MZ, et al.

Cell Rep. 2015 Jan 13;10(2):148-61. doi: 10.1016/j.celrep.2014.12.015. Epub 2014 Dec 31.

PubMed [citation]
PMID:
25558065

Phenotype variability of infantile-onset multisystem neurologic, endocrine, and pancreatic disease IMNEPD.

Picker-Minh S, Mignot C, Doummar D, Hashem M, Faqeih E, Josset P, Dubern B, Alkuraya FS, Kraemer N, Kaindl AM.

Orphanet J Rare Dis. 2016 Apr 29;11(1):52. doi: 10.1186/s13023-016-0433-z.

PubMed [citation]
PMID:
27129381
PMCID:
PMC4850685
See all PubMed Citations (4)

Details of each submission

From OMIM, SCV000212240.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In a 10-year-old boy (family 13DG0215), born of consanguineous parents, with infantile-onset multisystem neurologic, endocrine, and pancreatic disease-1 (IMNEPD1; 616263), Alazami et al. (2015) identified a homozygous c.254A-C transversion in the PTRH2 gene, resulting in a gln85-to-pro (Q85P) substitution. A brother was similarly affected. Functional studies of the variant were not performed. The patient had global developmental delay, hypotonia, hearing loss, and ataxia; pancreatic exocrine dysfunction was not reported. The patient was part of a large cohort of 143 multiplex consanguineous families with various neurodevelopmental disorders who underwent whole-exome sequencing.

Picker-Minh et al. (2016) identified homozygosity for the c.254A-C transversion (c.254A-C, NM_016077.4) in exon 2 of the PTRH2 gene, resulting in a Q85P substitution, in 5 patients from 2 unrelated highly consanguineous kindreds of Tunisian and Saudi Arabian descent with IMNEPD1. Fibroblasts derived from 1 of the patients showed normal PTRH2 mRNA levels, but decreased protein levels.

Sharkia et al. (2017) identified homozygosity for the Q85P mutation in the PTRH2 gene in 3 sibs, born of consanguineous Arab parents, with IMNEPD1. The mutation, which was found by a combination of homozygosity mapping and exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. Functional studies of the variant and studies of patient cells were not performed. Clinical variability was observed.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV002019564.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004804830.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 6, 2024