APCDD1

APC down-regulated 1

Basic information

Region (hg38): 18:10454635-10489949

Links

ENSG00000154856 ∙ NCBI:147495 ∙ OMIM:607479 ∙ HGNC:15718 ∙ Uniprot:Q8J025 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypotrichosis simplex (Supportive), mode of inheritance: AD
• hypotrichosis 1 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypotrichosis 1	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	Dermatologic	10878665; 20393562; 22512811

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the APCDD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APCDD1 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				10	9	19
missense			50	4	5	59
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					17	17
Total	0	0	50	15	31

Variants in APCDD1

This is a list of pathogenic ClinVar variants found in the APCDD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-10454963-C-G			Benign (Jun 18, 2021)
18-10454991-C-T		not specified	Uncertain significance (Oct 12, 2022)
18-10455003-C-G			Uncertain significance (Jul 17, 2022)
18-10455007-T-G		Hypotrichosis 1	Pathogenic (Oct 01, 2012)
18-10455080-A-G			Benign (Nov 10, 2018)
18-10455136-C-T			Benign (Nov 10, 2018)
18-10468318-A-G			Benign (Jun 18, 2021)
18-10468330-A-G			Benign (Jun 18, 2021)
18-10468456-C-T			Benign (Jan 31, 2024)
18-10468489-C-T		not specified	Uncertain significance (Aug 08, 2023)
18-10468580-A-T		not specified	Uncertain significance (May 10, 2024)
18-10468599-A-C		APCDD1-related disorder	Benign (Jan 17, 2023)
18-10468605-C-G		not specified	Uncertain significance (Jul 20, 2021)
18-10468638-C-T		APCDD1-related disorder	Likely benign (Oct 12, 2020)
18-10468652-G-A			Uncertain significance (Apr 07, 2023)
18-10471287-A-C			Benign (Jun 18, 2021)
18-10471524-G-A			Benign (Dec 18, 2023)
18-10471525-C-T			Likely benign (Mar 27, 2022)
18-10471628-G-A		not specified	Uncertain significance (Jun 16, 2023)
18-10471672-C-T		not specified	Uncertain significance (Mar 01, 2024)
18-10471679-G-A		not specified	Uncertain significance (Jan 08, 2024)
18-10471709-C-T		not specified	Uncertain significance (Jan 11, 2023)
18-10471719-C-G		not specified	Uncertain significance (May 30, 2024)
18-10471735-G-A			Benign (Jan 29, 2024)
18-10471767-C-T			Benign (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APCDD1	protein_coding	protein_coding	ENST00000355285	5	35321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00732	0.990	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.482	291	315	0.924	0.0000211	3369
Missense in Polyphen		120	129	0.93023		1373
Synonymous	-0.952	146	132	1.11	0.00000967	1025
Loss of Function	2.59	7	19.3	0.363	0.00000102	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000202	0.000202
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000793	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negative regulator of the Wnt signaling pathway. Inhibits Wnt signaling in a cell-autonomous manner and functions upstream of beta-catenin. May act via its interaction with Wnt and LRP proteins. May play a role in colorectal tumorigenesis. {ECO:0000269|PubMed:12384519, ECO:0000269|PubMed:20393562}.
• Disease: DISEASE: Hypotrichosis 1 (HYPT1) [MIM:605389]: A rare form of non- syndromic hereditary hypotrichosis without characteristic hair shaft anomalies. Affected individuals typically show normal hair at birth, but hair loss and thinning of the hair shaft start during early childhood and progress with age. {ECO:0000269|PubMed:20393562}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.555
• rvis_EVS: -1.37
• rvis_percentile_EVS: 4.45

Haploinsufficiency Scores

• pHI: 0.210
• hipred: Y
• hipred_score: 0.517
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.301

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apcdd1

Gene ontology

• Biological process: hair follicle development;Wnt signaling pathway;negative regulation of Wnt signaling pathway;astrocyte cell migration
• Cellular component: integral component of plasma membrane
• Molecular function: protein binding;Wnt-protein binding;identical protein binding