SAPCD1

suppressor APC domain containing 1

Basic information

Region (hg38): 6:31762655-31764850

Previous symbols: [ "C6orf26" ]

Links

ENSG00000228727 ∙ NCBI:401251 ∙ ∙ HGNC:13938 ∙ Uniprot:Q5SSQ6 ∙ 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 SAPCD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAPCD1 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			6	5	1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	5	1

Variants in SAPCD1

This is a list of pathogenic ClinVar variants found in the SAPCD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31763134-G-A		not specified	Likely benign (Oct 05, 2021)
6-31763545-C-A		not specified	Uncertain significance (Sep 16, 2021)
6-31764104-C-T		not specified	Benign (Mar 29, 2016)
6-31764155-A-T		not specified	Uncertain significance (Nov 22, 2023)
6-31764273-C-T		not specified	Likely benign (Jun 02, 2023)
6-31764284-A-G		not specified	Uncertain significance (Oct 29, 2021)
6-31764293-A-G		not specified	Likely benign (Apr 07, 2023)
6-31764311-G-A		not specified	Uncertain significance (Jan 23, 2023)
6-31764482-T-C		not specified	Likely benign (Jul 12, 2022)
6-31764490-C-T		not specified	Likely benign (Dec 21, 2023)
6-31764506-G-T		not specified	Uncertain significance (Dec 12, 2023)
6-31764523-C-T		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAPCD1	protein_coding	protein_coding	ENST00000415669	5	2053

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.81e-7	0.139	125527	0	217	125744	0.000863

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.282	84	91.6	0.917	0.00000478	1130
Missense in Polyphen		18	20.605	0.87358		305
Synonymous	0.766	31	36.9	0.840	0.00000176	357
Loss of Function	-0.179	10	9.41	1.06	4.87e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000414	0.000395
Ashkenazi Jewish	0.000202	0.000198
East Asian	0.000109	0.000109
Finnish	0.000607	0.000601
European (Non-Finnish)	0.00169	0.00164
Middle Eastern	0.000109	0.000109
South Asian	0.0000986	0.0000980
Other	0.000497	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.44
• rvis_percentile_EVS: 95.05

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sapcd1
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)