SAPCD2

protein-coding

suppressor APC domain containing 2

Gene summary

Involved in negative regulation of protein localization to cell cortex and positive regulation of cell population proliferation. Located in several cellular components, including apical cortex; apical junction complex; and nuclear lumen. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C9orf140

MANE transcript

NM_178448.4

Inheritance

—

ClinVar variants

U:76B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr9:137,062,127-137,070,557

External References & Databases

Ensembl (ENSG00000186193)

Transcript & Mutation Effects

hg38 • Region Span ~8.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SAPCD2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 76

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178448.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			75 clinvar	3 clinvar		78
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	4	0	80

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178448.4	RefSeq	NP_848543.2	6	MANE Select
ENST00000409687.5	Ensembl	ENSP00000386348.3	6	MANE Select
ENST00000879034.1	Ensembl	ENSP00000549093.1	7	Standard
ENST00000879034.2	Ensembl	ENSP00000549093.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

protein binding

Cellular Component

nucleus
nucleolus
cytosol
bicellular tight junction
apical plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409687
Coding exons: 6
Length: 8460
Individuals with no LoFs: 125549
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125568
p: 0.0000757

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.835	131	161	0.815	0.0000107	2410
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00034	0.00033	rare
Finnish	0.00015	0.00014	rare
European (Non-Finnish)	0.000049	0.000044	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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