NM_138927.4(SON):c.4151_4174del (p.Leu1384_Val1391del) AND ZTTK syndrome

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: May 4, 2022
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:: RCV000755182.2

Allele description [Variation Report for NM_138927.4(SON):c.4151_4174del (p.Leu1384_Val1391del)]

NM_138927.4(SON):c.4151_4174del (p.Leu1384_Val1391del)

Gene:

SON:SON DNA and RNA binding protein [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

21q22.11

Genomic location:

Preferred name:

NM_138927.4(SON):c.4151_4174del (p.Leu1384_Val1391del)

HGVS:

NC_000021.9:g.33553382_33553405del
NG_052981.1:g.15345_15368del
NM_001291411.2:c.4151_4174del
NM_001291412.3:c.245-3774_245-3751del
NM_032195.3:c.4151_4174del
NM_138927.4:c.4151_4174delMANE SELECT
NP_001278340.2:p.Leu1384_Val1391del
NP_115571.3:p.Leu1384_Val1391del
NP_620305.3:p.Leu1384_Val1391del
NC_000021.8:g.34925681_34925704del
NC_000021.8:g.34925688_34925711del
NC_000021.9:g.33553375_33553398delACTGTCCTGGAGCCTTCGGTTGTG
NM_138927.2:c.4151_4174del
NR_103797.2:n.4206_4229del

Links:

dbSNP: rs769691894

NCBI 1000 Genomes Browser:

rs769691894

Molecular consequence:

NM_001291411.2:c.4151_4174del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_032195.3:c.4151_4174del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_138927.4:c.4151_4174del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001291412.3:c.245-3774_245-3751del - intron variant - [Sequence Ontology: SO:0001627]
NR_103797.2:n.4206_4229del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: ZTTK syndrome (ZTTKS)
Synonyms:: ZTTK MULTIPLE CONGENITAL ANOMALIES-MENTAL RETARDATION SYNDROME; ZHU-TOKITA-TAKENOUCHI-KIM SYNDROME
Identifiers:: MONDO: MONDO:0014936; MedGen: C4310696; OMIM: 617140

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000883011	University of Washington Center for Mendelian Genomics, University of Washington	no assertion criteria provided	Likely pathogenic (Sep 1, 2016)	unknown	research	PubMed (1) [See all records that cite this PMID]
SCV002519799	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Pathogenic (May 4, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000883011

University of Washington Center for Mendelian Genomics, University of Washington

no assertion criteria provided

Likely pathogenic
(Sep 1, 2016)

unknown

research

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

SCV002519799

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2019)

Pathogenic
(May 4, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	1	not provided	not provided	not provided	not provided	research

Citations

PubMed

De Novo Mutations in SON Disrupt RNA Splicing of Genes Essential for Brain Development and Metabolism, Causing an Intellectual-Disability Syndrome.

Kim JH, Shinde DN, Reijnders MRF, Hauser NS, Belmonte RL, Wilson GR, Bosch DGM, Bubulya PA, Shashi V, Petrovski S, Stone JK, Park EY, Veltman JA, Sinnema M, Stumpel CTRM, Draaisma JM, Nicolai J; University of Washington Center for Mendelian Genomics., Yntema HG, Lindstrom K, de Vries BBA, Jewett T, et al.

Am J Hum Genet. 2016 Sep 1;99(3):711-719. doi: 10.1016/j.ajhg.2016.06.029. Epub 2016 Aug 18.

PubMed [citation]

PMID:: 27545680
PMCID:: PMC5011044

Details of each submission

From University of Washington Center for Mendelian Genomics, University of Washington, SCV000883011.1

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

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

From Mendelics, SCV002519799.1

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

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

Last Updated: Feb 20, 2024

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