SAPCD2

suppressor APC domain containing 2

Basic information

Region (hg38): 9:137062127-137070557

Previous symbols: [ "C9orf140" ]

Links

ENSG00000186193 ∙ NCBI:89958 ∙ OMIM:612057 ∙ HGNC:28055 ∙ Uniprot:Q86UD0 ∙ 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 SAPCD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAPCD2 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				1		1
missense			42	3		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	4	0

Variants in SAPCD2

This is a list of pathogenic ClinVar variants found in the SAPCD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-137064741-T-C		not specified	Uncertain significance (Nov 17, 2023)
9-137064886-C-T		not specified	Uncertain significance (Aug 23, 2021)
9-137065080-G-A		not specified	Uncertain significance (Mar 20, 2023)
9-137065148-C-T		not specified	Likely benign (Sep 06, 2022)
9-137065149-G-A		not specified	Uncertain significance (Mar 08, 2024)
9-137065173-C-T		not specified	Uncertain significance (Jan 19, 2024)
9-137065524-C-T		not specified	Likely benign (Aug 02, 2023)
9-137065541-C-G		not specified	Uncertain significance (Oct 20, 2023)
9-137065550-C-T		not specified	Uncertain significance (Dec 07, 2021)
9-137065556-C-T		not specified	Uncertain significance (Apr 18, 2023)
9-137065593-C-T		not specified	Uncertain significance (Feb 01, 2023)
9-137065604-G-A		not specified	Uncertain significance (May 03, 2023)
9-137065653-C-G		not specified	Uncertain significance (Jan 26, 2022)
9-137065662-G-C		not specified	Uncertain significance (Feb 06, 2023)
9-137066276-C-T		not specified	Uncertain significance (Jul 27, 2024)
9-137066279-C-T		not specified	Uncertain significance (Jun 24, 2022)
9-137066302-C-T		not specified	Uncertain significance (Jul 09, 2024)
9-137066317-C-T		not specified	Uncertain significance (Oct 14, 2021)
9-137066365-G-A		not specified	Uncertain significance (Aug 21, 2024)
9-137066371-G-A		not specified	Uncertain significance (Aug 04, 2023)
9-137069910-G-A		not specified	Uncertain significance (Nov 09, 2024)
9-137069918-C-T			Likely benign (Dec 01, 2022)
9-137069934-C-A		not specified	Uncertain significance (Nov 20, 2024)
9-137069961-G-A		not specified	Uncertain significance (Aug 09, 2021)
9-137069979-A-G		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAPCD2	protein_coding	protein_coding	ENST00000409687	6	8460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00394	0.962	125549	0	19	125568	0.0000757

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.835	131	161	0.815	0.0000107	2410
Missense in Polyphen		36	52.226	0.68932		723
Synonymous	0.470	64	69.0	0.928	0.00000440	881
Loss of Function	1.86	6	13.3	0.451	8.44e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000183	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.000337	0.000326
Finnish	0.000150	0.000139
European (Non-Finnish)	0.0000486	0.0000441
Middle Eastern	0.000337	0.000326
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in planar mitotic spindle orientation in retinal progenitor cells (RPCs) and promotes the production of symmetric terminal divisions (By similarity). Negatively regulates the mitotic apical cortex localization of GPSM2 (PubMed:26766442). Involved also in positive regulation of cell proliferation and tumor cell growth (PubMed:23576022, PubMed:23704824). {ECO:0000250|UniProtKB:Q9D818, ECO:0000269|PubMed:23576022, ECO:0000269|PubMed:23704824, ECO:0000269|PubMed:26766442}.

Recessive Scores

• pRec: 0.108

Haploinsufficiency Scores

• pHI: 0.244
• hipred: N
• hipred_score: 0.208
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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	High	Medium	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Sapcd2
• Phenotype: normal phenotype

Gene ontology

• Biological process: establishment of mitotic spindle orientation;positive regulation of cell population proliferation;regulation of establishment of planar polarity;symmetric cell division;negative regulation of protein localization to cell cortex
• Cellular component: nucleus;nucleolus;cytosol;bicellular tight junction;apical plasma membrane;apical junction complex;apical cortex
• Molecular function: protein binding