Single allele AND Developmental delay with variable intellectual impairment and behavioral abnormalities

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 13, 2021
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:: RCV001391668.1

Allele description [Variation Report for Single allele]

Genes:

ARFGAP3:ADP ribosylation factor GTPase activating protein 3 [Gene - OMIM - HGNC]
ATP5MGL:ATP synthase membrane subunit g like [Gene - HGNC]
BIK:BCL2 interacting killer [Gene - OMIM - HGNC]
POLDIP3:DNA polymerase delta interacting protein 3 [Gene - OMIM - HGNC]
NDUFA6:NADH:ubiquinone oxidoreductase subunit A6 [Gene - OMIM - HGNC]
NFAM1:NFAT activating protein with ITAM motif 1 [Gene - OMIM - HGNC]
PHETA2:PH domain containing endocytic trafficking adaptor 2 [Gene - OMIM - HGNC]
TTLL1:TTL family tubulin polyglutamylase complex subunit L1 [Gene - OMIM - HGNC]
A4GALT:alpha 1,4-galactosyltransferase (P blood group) [Gene - OMIM - HGNC]
NAGA:alpha-N-acetylgalactosaminidase [Gene - OMIM - HGNC]
CYP2D6:cytochrome P450 family 2 subfamily D member 6 [Gene - OMIM - HGNC]
CYB5R3:cytochrome b5 reductase 3 [Gene - OMIM - HGNC]
MCAT:malonyl-CoA-acyl carrier protein transacylase [Gene - OMIM - HGNC]
PACSIN2:protein kinase C and casein kinase substrate in neurons 2 [Gene - OMIM - HGNC]
RRP7A:ribosomal RNA processing 7 homolog A [Gene - OMIM - HGNC]
SERHL2:serine hydrolase like 2 [Gene - OMIM - HGNC]
SCUBE1:signal peptide, CUB domain and EGF like domain containing 1 [Gene - OMIM - HGNC]
SMDT1:single-pass membrane protein with aspartate rich tail 1 [Gene - OMIM - HGNC]
TCF20:transcription factor 20 [Gene - OMIM - HGNC]
TSPO:translocator protein [Gene - OMIM - HGNC]
TTLL12:tubulin tyrosine ligase like 12 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

22q13.2

Genomic location:

Chr22: 42440000 - 43780000 (on Assembly GRCh37)

HGVS:

NC_000022.10:g.42440000_43780000del

Condition(s)

Name:: Developmental delay with variable intellectual impairment and behavioral abnormalities
Identifiers:: MONDO: MONDO:0032745; MedGen: C5193092; OMIM: 618430

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001593292	Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (May 13, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31690835, 30819258

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001593292

Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(May 13, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).

Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL.

Genet Med. 2020 Feb;22(2):245-257. doi: 10.1038/s41436-019-0686-8. Epub 2019 Nov 6. Erratum in: Genet Med. 2021 Nov;23(11):2230. doi: 10.1038/s41436-021-01150-9.

PubMed [citation]

PMID:: 31690835
PMCID:: PMC7313390

De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome.

Vetrini F, McKee S, Rosenfeld JA, Suri M, Lewis AM, Nugent KM, Roeder E, Littlejohn RO, Holder S, Zhu W, Alaimo JT, Graham B, Harris JM, Gibson JB, Pastore M, McBride KL, Komara M, Al-Gazali L, Al Shamsi A, Fanning EA, Wierenga KJ, Scott DA, et al.

Genome Med. 2019 Feb 28;11(1):12. doi: 10.1186/s13073-019-0623-0. Erratum in: Genome Med. 2019 Mar 25;11(1):16. doi: 10.1186/s13073-019-0630-1.

PubMed [citation]

PMID:: 30819258
PMCID:: PMC6393995

Details of each submission

From Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, SCV001593292.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	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: Apr 23, 2022

ClinVar

Relating variation to medicine