NM_001282531.3(ADNP):c.1222_1223del (p.Lys408fs) AND ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder - ClinVar

NM_001282531.3(ADNP):c.1222_1223del (p.Lys408fs) AND ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Dec 1, 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:: RCV000170480.5

Allele description [Variation Report for NM_001282531.3(ADNP):c.1222_1223del (p.Lys408fs)]

NM_001282531.3(ADNP):c.1222_1223del (p.Lys408fs)

Gene:

ADNP:activity dependent neuroprotector homeobox [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

20q13.13

Genomic location:

Preferred name:

NM_001282531.3(ADNP):c.1222_1223del (p.Lys408fs)

HGVS:

NC_000020.11:g.50893492_50893493del
NG_034200.1:g.42499_42500del
NM_001282531.3:c.1222_1223delMANE SELECT
NM_001282532.2:c.1222_1223del
NM_001347511.2:c.1222_1223del
NM_015339.5:c.1222_1223del
NM_181442.4:c.1222_1223del
NP_001269460.1:p.Lys408fs
NP_001269461.1:p.Lys408fs
NP_001334440.1:p.Lys408fs
NP_056154.1:p.Lys408fs
NP_852107.1:p.Lys408fs
NC_000020.10:g.49510029_49510030del

Protein change:

K408fs

Links:

OMIM: 611386.0008; dbSNP: rs1555810376

NCBI 1000 Genomes Browser:

rs1555810376

Molecular consequence:

NM_001282531.3:c.1222_1223del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001282532.2:c.1222_1223del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001347511.2:c.1222_1223del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015339.5:c.1222_1223del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_181442.4:c.1222_1223del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder
Synonyms:: Helsmoortel-Van der Aa Syndrome
Identifiers:: MONDO: MONDO:0014379; MedGen: C4014538; Orphanet: 404448; OMIM: 615873

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000222907	OMIM	no assertion criteria provided	Pathogenic (Mar 12, 2015)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV003935037	Eurofins-Biomnis	criteria provided, single submitter (Accession Criteria ClinVar Biomnis)	Likely pathogenic (Dec 1, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000222907

OMIM

no assertion criteria provided

Pathogenic
(Mar 12, 2015)

germline

literature only

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

SCV003935037

Eurofins-Biomnis

criteria provided, single submitter

(Accession Criteria ClinVar Biomnis)

Likely pathogenic
(Dec 1, 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	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

Large-scale discovery of novel genetic causes of developmental disorders.

Deciphering Developmental Disorders Study..

Nature. 2015 Mar 12;519(7542):223-8. doi: 10.1038/nature14135. Epub 2014 Dec 24.

PubMed [citation]

PMID:: 25533962
PMCID:: PMC5955210

Details of each submission

From OMIM, SCV000222907.2

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

Description

In a male patient with Helsmoortel-Van der Aa syndrome (HVDAS; 615873), the Deciphering Developmental Disorders Study (2015) identified a heterozygous de novo 2-bp deletion of a TT at chromosome coordinate g.49,510,027 in the ADNP gene (chr20.49,510,027delTT). The authors described the mutation as an indel (CTTT/CT) between coordinates g.49,510,027 and g.49,510,031. The patient had global developmental delay, generalized neonatal hypotonia, bilateral ptosis, plagiocephaly, first-degree microtia, and respiratory distress.

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

From Eurofins-Biomnis, SCV003935037.1

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

Last Updated: Jul 1, 2023

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