ADNP

activity dependent neuroprotector homeobox, the group of ZF class homeoboxes and pseudogenes

Basic information

Region (hg38): 20:50888916-50931437

Links

ENSG00000101126NCBI:23394OMIM:611386HGNC:15766Uniprot:Q9H2P0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder (Strong), mode of inheritance: AD
  • ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder (Definitive), mode of inheritance: AD
  • ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder (Supportive), mode of inheritance: Unknown
  • ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Helsmoortel-van der Aa syndromeADCardiovascularIndividuals have been described with congenital heart anomalies, and awareness may enable early diagnosis and managementCardiovascular; Craniofacial; Musculoskeletal; Neurologic24531329; 25057125

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADNP gene.

  • not provided (59 variants)
  • ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder (37 variants)
  • Inborn genetic diseases (13 variants)
  • ADNP-related disorder (5 variants)
  • Intellectual disability (1 variants)
  • See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADNP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
32
clinvar
83
clinvar
18
clinvar
133
missense
5
clinvar
259
clinvar
63
clinvar
6
clinvar
333
nonsense
24
clinvar
6
clinvar
30
start loss
2
clinvar
1
clinvar
3
frameshift
60
clinvar
24
clinvar
3
clinvar
87
inframe indel
12
clinvar
3
clinvar
15
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
2
splice region
4
4
non coding
1
clinvar
11
clinvar
5
clinvar
5
clinvar
22
Total 87 37 318 154 29

Variants in ADNP

This is a list of pathogenic ClinVar variants found in the ADNP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
20-50889829-C-T Likely benign (Oct 01, 2024)2652398
20-50889934-G-A Likely benign (Apr 01, 2024)3234565
20-50889959-T-C Uncertain significance (Oct 01, 2024)3389957
20-50891355-T-G ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder Benign (Jul 14, 2021)1189012
20-50891406-T-TA Likely pathogenic (Jan 31, 2017)545057
20-50891410-C-T ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder Uncertain significance (Oct 24, 2019)931701
20-50891412-T-C Uncertain significance (Feb 18, 2020)1312755
20-50891414-T-C Likely benign (Dec 15, 2024)2993454
20-50891421-C-T Uncertain significance (Nov 19, 2021)1446926
20-50891422-T-C Uncertain significance (Oct 31, 2023)2692581
20-50891428-T-C Uncertain significance (Oct 30, 2024)3657930
20-50891431-C-T Uncertain significance (Nov 12, 2024)3625167
20-50891433-C-A Inborn genetic diseases Uncertain significance (Jul 26, 2022)1729749
20-50891434-C-T not specified Uncertain significance (Aug 24, 2023)2581349
20-50891435-G-A not specified • Inborn genetic diseases • ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder • ADNP-related disorder Benign/Likely benign (Jan 28, 2025)434090
20-50891434-C-CGG ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder not provided (-)225224
20-50891448-T-C ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder Uncertain significance (Apr 23, 2021)2438882
20-50891452-T-C Uncertain significance (May 06, 2024)2829629
20-50891456-C-A Inborn genetic diseases Conflicting classifications of pathogenicity (Jan 06, 2025)1729487
20-50891462-T-C Likely benign (May 23, 2024)3670276
20-50891463-A-G Uncertain significance (Apr 20, 2024)3650456
20-50891465-T-TC ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder Uncertain significance (May 21, 2018)546371
20-50891467-C-G Uncertain significance (Apr 04, 2024)3371960
20-50891466-C-CCAT ADNP-related disorder Uncertain significance (Oct 17, 2024)2784727
20-50891473-T-A Uncertain significance (Mar 13, 2024)3693715

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ADNPprotein_codingprotein_codingENST00000396029 342374
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.00000489125733061257390.0000239
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.074395790.7580.00003007343
Missense in Polyphen57189.870.30022552
Synonymous-3.922882151.340.00001182066
Loss of Function5.61138.70.02590.00000227486

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001230.000123
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00002640.0000264
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Potential transcription factor. May mediate some of the neuroprotective peptide VIP-associated effects involving normal growth and cancer proliferation.;

Recessive Scores

pRec
0.133

Intolerance Scores

loftool
0.00689
rvis_EVS
-1.41
rvis_percentile_EVS
4.13

Haploinsufficiency Scores

pHI
0.904
hipred
Y
hipred_score
0.591
ghis
0.689

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.881

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Adnp
Phenotype
embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Zebrafish Information Network

Gene name
adnpa
Affected structure
blood cell
Phenotype tag
abnormal
Phenotype quality
decreased amount

Gene ontology

Biological process
regulation of transcription by RNA polymerase II;short-term memory;response to carbohydrate;response to inorganic substance;negative regulation of gene expression;regulation of protein ADP-ribosylation;cGMP-mediated signaling;cellular response to extracellular stimulus;negative regulation of protein binding;activation of protein kinase activity;nitric oxide homeostasis;negative regulation of neuron apoptotic process;estrous cycle;positive regulation of axon extension;positive regulation of peptidyl-tyrosine phosphorylation;negative regulation of synaptic transmission;positive regulation of synapse assembly
Cellular component
extracellular space;nucleus;cytoplasm;axon;dendrite;neuronal cell body
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;chromatin binding;copper ion binding;protein binding;peptide binding;beta-tubulin binding