APCDD1L

APC down-regulated 1 like

Basic information

Region (hg38): 20:58459101-58515399

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.

• not_specified (89 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. These statistics are base on transcript: NM_000153360.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			86	3		89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	86	3	0

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