AHDC1

AT-hook DNA binding motif containing 1

Basic information

Region (hg38): 1:27534035-27604431

Links

ENSG00000126705 ∙ NCBI:27245 ∙ OMIM:615790 ∙ HGNC:25230 ∙ Uniprot:Q5TGY3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome (Strong), mode of inheritance: AD
• AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome (Strong), mode of inheritance: AD
• AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome (Supportive), mode of inheritance: AD
• AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome (Strong), mode of inheritance: AD
• AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Xia-Gibbs syndrome	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic; Craniofacial; Neurologic	24791903

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AHDC1 gene.

• not provided (53 variants)
• AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome (45 variants)
• Inborn genetic diseases (6 variants)
• Intellectual disability;Global developmental delay;Sleep apnea;Neonatal hypotonia;Delayed speech and language development (3 variants)
• Hypotonia;Sleep apnea;Delayed speech and language development (3 variants)
• Neurodevelopmental abnormality (2 variants)
• AHDC1-related disorder (1 variants)
• Neurodevelopmental disorder (1 variants)
• Neurodevelopmental delay (1 variants)
• See cases (1 variants)
• Cerebral visual impairment and intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AHDC1 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			3	311	25	339
missense		3	453	132	17	605
nonsense	26	9	1			36
start loss						0
frameshift	67	20	5			92
inframe indel			8	5	1	14
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			1	2	1	4
Total	93	32	472	450	44

Variants in AHDC1

This is a list of pathogenic ClinVar variants found in the AHDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-27547319-G-A		AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome	Benign/Likely benign (May 01, 2024)
1-27547326-G-C			Uncertain significance (Jan 13, 2023)
1-27547327-T-C		Inborn genetic diseases	Uncertain significance (May 24, 2024)
1-27547334-G-A		AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome	Benign (Nov 01, 2024)
1-27547347-G-A			Uncertain significance (Oct 03, 2023)
1-27547351-T-C			Uncertain significance (Dec 13, 2023)
1-27547355-C-A			Likely benign (Mar 03, 2024)
1-27547362-A-AAGCC			Uncertain significance (Oct 23, 2023)
1-27547364-G-A			Likely benign (Aug 10, 2022)
1-27547366-C-T			Uncertain significance (Apr 27, 2023)
1-27547367-G-A			Likely benign (Oct 03, 2023)
1-27547377-C-A			Uncertain significance (Dec 01, 2022)
1-27547384-C-T			Uncertain significance (Nov 01, 2022)
1-27547398-G-A		Inborn genetic diseases • AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome	Conflicting classifications of pathogenicity (May 20, 2023)
1-27547399-C-A			Likely benign (Aug 09, 2022)
1-27547429-C-T			Uncertain significance (Nov 05, 2024)
1-27547430-G-A			Likely benign (Nov 11, 2024)
1-27547437-T-A		AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome	Uncertain significance (May 28, 2019)
1-27547442-G-A			Likely benign (Apr 13, 2022)
1-27547442-G-C			Likely benign (Sep 14, 2024)
1-27547443-G-A		not specified	Uncertain significance (May 06, 2024)
1-27547449-A-T		Inborn genetic diseases	Uncertain significance (Jun 20, 2023)
1-27547452-G-A		Inborn genetic diseases • Spastic ataxia	Benign/Likely benign (Apr 18, 2024)
1-27547460-C-T			Likely benign (Jun 20, 2024)
1-27547461-G-A			Likely benign (Aug 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AHDC1	protein_coding	protein_coding	ENST00000374011	1	70397

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	8.53e-7	125148	0	1	125149	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.86	764	1.02e+3	0.748	0.0000727	10021
Missense in Polyphen		85	120.67	0.7044		1043
Synonymous	-0.567	488	472	1.03	0.0000351	3692
Loss of Function	5.78	0	38.9	0.00	0.00000231	434

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000545	0.0000545
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Mental retardation, autosomal dominant 25 (MRD25) [MIM:615829]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD25 additional features include mild dysmorphism, hypotonia, delayed psychomotor development with absent or poor expressive language, hypoplasia of the corpus callosum, simplified gyral pattern, and delayed myelination. {ECO:0000269|PubMed:24791903}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Mesodermal Commitment Pathway (Consensus)

Intolerance Scores

• loftool: 0.0110
• rvis_EVS: -1.1
• rvis_percentile_EVS: 6.98

Haploinsufficiency Scores

• pHI: 0.0929
• hipred: Y
• hipred_score: 0.675
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.526

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ahdc1

Gene ontology

• Molecular function: DNA binding