SCAND3

protein-coding

SCAN domain containing 3, the group of SCAN domain containing

Gene summary

Predicted to enable nucleic acid binding activity. Involved in positive regulation of cell cycle and positive regulation of epithelial cell proliferation. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF305P2
ZNF452
SCAND3
ZBED9

MANE transcript

NM_052923.2

Inheritance

—

ClinVar variants

U:80B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr6:28,570,535-28,616,212

External References & Databases

Ensembl (ENSG00000232040)

Transcript & Mutation Effects

hg38 • Region Span ~45.7 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 SCAND3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 79

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052923.2. 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			1 clinvar	1 clinvar		2
missense			79 clinvar	2 clinvar		81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	80	3	0	83

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052923.2	RefSeq	NP_443155.1	4	MANE Select
ENST00000452236.3	Ensembl	ENSP00000395259.2	4	MANE Select
NM_001329616.2	RefSeq	NP_001316545.1	3	Standard
ENST00000646382.1	Ensembl	ENSP00000494942.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated
DNA integration

Molecular Function

nucleic acid binding
DNA-binding transcription factor activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000452236
Coding exons: 4
Length: 44583
Individuals with no LoFs: 125514
Homozygous LoFs: 1
Heterozygous LoFs: 233
Defined: 125748
p: 0.000931

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.39	495	669	0.740	0.0000333	8774
Missense (PolyPhen)		148	213.85	0.69207		3015
Synonymous	2.42	189	236	0.800	0.0000111	2448
Loss of Function	3.36	22	46.8	0.470	0.00000248	660

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.0017	0.0016	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.0064	0.0064	notable
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00033	0.00033	rare
South Asian	0.00042	0.00039	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0942

Intolerance Scores

RVIS EVS: -0.95
RVIS percentile EVS: 9.32

Essentials

Essential (gene trap): N