NM_001372044.2(SHANK3):c.4600G>A (p.Gly1534Arg) AND Phelan-McDermid syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 10, 2023
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:: RCV003127574.2

Allele description [Variation Report for NM_001372044.2(SHANK3):c.4600G>A (p.Gly1534Arg)]

NM_001372044.2(SHANK3):c.4600G>A (p.Gly1534Arg)

Gene:

SHANK3:SH3 and multiple ankyrin repeat domains 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q13.33

Genomic location:

Preferred name:

NM_001372044.2(SHANK3):c.4600G>A (p.Gly1534Arg)

Other names:

chr22:51160636G>A

HGVS:

NC_000022.11:g.50722208G>A
NG_070230.1:g.57992G>A
NM_001372044.2:c.4600G>AMANE SELECT
NP_001358973.1:p.Gly1534Arg
NC_000022.10:g.51160636G>A

Protein change:

G1534R

Links:

dbSNP: rs1440735830

NCBI 1000 Genomes Browser:

rs1440735830

Molecular consequence:

NM_001372044.2:c.4600G>A - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

probably no functional consequence

Observations:

Condition(s)

Name:: Phelan-McDermid syndrome
Synonyms:: TELOMERIC 22q13 MONOSOMY SYNDROME; 22q13.3 deletion syndrome; Chromosome 22q13.3 deletion syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011652; MedGen: C1853490; Orphanet: 48652; OMIM: 606232

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003803637	Laboratory of Functional Genomics, Research Centre for Medical Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 10, 2023)	paternal, unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003803637

Laboratory of Functional Genomics, Research Centre for Medical Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 10, 2023)

paternal, unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	no	1	not provided	not provided	not provided	not provided	clinical testing
not provided	paternal	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Laboratory of Functional Genomics, Research Centre for Medical Genetics, SCV003803637.1

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

Description

Proband is a three year-old boy with a psycho-speech delay. Heterozygous missense variant NM_001372044.2 (SHANK3):c.4600G>A was found by WGS. Segregation analysis by Sanger sequencing revealed the variant in proband and his healthy father. According to ACMG, the variant meets the criteria PM2, PP2, BS4 and is concidered as a variant of uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	paternal	yes	not provided	not provided	not provided		1	not provided	not provided	not provided
2	unknown	no	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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