APCDD1L

APC down-regulated 1 like

Basic information

Region (hg38): 20:58459100-58515399

Links

ENSG00000198768 ∙ NCBI:164284 ∙ ∙ HGNC:26892 ∙ Uniprot:Q8NCL9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the APCDD1L gene.

• Inborn genetic diseases (32 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APCDD1L 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						0
missense			30	2		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	0

Variants in APCDD1L

This is a list of pathogenic ClinVar variants found in the APCDD1L region.

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

Position	Type	Phenotype	Significance	ClinVar
20-58460804-G-A		not specified	Uncertain significance (Nov 02, 2023)
20-58460915-C-T		not specified	Uncertain significance (Dec 19, 2022)
20-58460945-G-T		not specified	Uncertain significance (Oct 06, 2023)
20-58460977-G-A		not specified	Uncertain significance (Nov 08, 2021)
20-58461011-C-T		not specified	Uncertain significance (Apr 08, 2022)
20-58461013-A-G		not specified	Uncertain significance (Jan 23, 2023)
20-58461034-A-G		not specified	Uncertain significance (Jun 26, 2023)
20-58461062-C-T		not specified	Uncertain significance (May 11, 2022)
20-58461092-G-C		not specified	Uncertain significance (May 17, 2023)
20-58461094-G-A		not specified	Uncertain significance (Mar 28, 2023)
20-58461149-C-T		not specified	Uncertain significance (May 05, 2023)
20-58461155-C-G		not specified	Uncertain significance (Apr 25, 2023)
20-58461257-C-T		not specified	Uncertain significance (Jun 21, 2022)
20-58461277-G-A		not specified	Uncertain significance (Oct 06, 2021)
20-58461409-A-G		not specified	Uncertain significance (Sep 16, 2021)
20-58461424-A-G		not specified	Uncertain significance (Sep 22, 2023)
20-58461491-C-T		not specified	Uncertain significance (Nov 17, 2022)
20-58461509-C-A		not specified	Uncertain significance (Aug 17, 2021)
20-58461514-C-T		not specified	Uncertain significance (Jan 31, 2024)
20-58461548-C-A		not specified	Uncertain significance (Nov 03, 2023)
20-58461548-C-T		not specified	Uncertain significance (Apr 07, 2022)
20-58461551-G-A		not specified	Uncertain significance (May 27, 2022)
20-58467111-C-A		not specified	Uncertain significance (Mar 16, 2022)
20-58467125-C-T		not specified	Likely benign (Feb 03, 2022)
20-58467356-G-A		not specified	Uncertain significance (Jun 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APCDD1L	protein_coding	protein_coding	ENST00000371149	4	56031

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0590	0.926	125666	0	24	125690	0.0000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.378	287	306	0.939	0.0000216	3085
Missense in Polyphen		110	104.97	1.0479		1144
Synonymous	0.662	131	141	0.929	0.0000102	1117
Loss of Function	2.11	4	11.8	0.338	5.63e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000222	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000736	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.0000276	0.0000264
Middle Eastern	0.000736	0.000707
South Asian	0.0000472	0.0000327
Other	0.000358	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.649
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.16

Haploinsufficiency Scores

• pHI: 0.442
• hipred: N
• hipred_score: 0.361
• ghis: 0.388

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

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

Gene ontology

• Cellular component: integral component of membrane