SAPCD1

Gene

suppressor APC domain containing 1

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

Previous symbols:

C6orf26

MANE transcript

NM_001039651.2

Inheritance

—

ClinVar variants

U:14B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.06

Max pathogenic AF

—

Genomic locus

chr6:31,762,656-31,764,850

External References & Databases

Ensembl (ENSG00000228727)

Transcript & Mutation Effects

hg38 • Region Span ~2.2 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 SAPCD1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 21

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001039651.2. 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						0
missense			14 clinvar	7 clinvar		21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	14	7	0	21

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001039651.2	RefSeq	NP_001034740.1	5	MANE Select
ENST00000415669.4	Ensembl	ENSP00000411948.2	5	MANE Select
ENST00000425424.4	Ensembl	ENSP00000413372.1	4	Standard
ENST00000425424.5	Ensembl	ENSP00000413372.1	4	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000415669
Coding exons: 5
Length: 2053
Individuals with no LoFs: 125527
Homozygous LoFs: 0
Heterozygous LoFs: 217
Defined: 125744
p: 0.000863

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.282	84	91.6	0.917	0.00000478	1130
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00033	0.00031	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00061	0.00060	rare
European (Non-Finnish)	0.0017	0.0016	notable
South Asian	0.000099	0.000098	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1.44
RVIS percentile EVS: 95.05

Essentials

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

Gene Damage Prediction

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