SCAND3

SCAN domain containing 3, the group of SCAN domain containing

Basic information

Region (hg38): 6:28570535-28616212

Previous symbols: [ "ZNF305P2", "ZNF452", "SCAND3", "ZBED9" ]

Links

ENSG00000232040 ∙ NCBI:114821 ∙ OMIM:615254 ∙ HGNC:13851 ∙ Uniprot:Q6R2W3 ∙ 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 SCAND3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAND3 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in SCAND3

This is a list of pathogenic ClinVar variants found in the SCAND3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-28574663-G-A		not specified	Uncertain significance (Jul 03, 2024)
6-28574703-G-T		not specified	Uncertain significance (Sep 01, 2021)
6-28574885-T-C		not specified	Uncertain significance (Jan 31, 2022)
6-28574897-C-T		not specified	Uncertain significance (Mar 25, 2024)
6-28575005-T-A		not specified	Uncertain significance (Apr 29, 2022)
6-28575112-C-G		not specified	Uncertain significance (Sep 16, 2021)
6-28575155-G-A		not specified	Uncertain significance (Sep 11, 2024)
6-28575193-C-T		not specified	Uncertain significance (Jun 10, 2024)
6-28575234-T-C		not specified	Uncertain significance (Dec 20, 2021)
6-28575239-G-T		not specified	Uncertain significance (Mar 22, 2023)
6-28575341-G-A		not specified	Uncertain significance (Nov 11, 2024)
6-28575347-A-G		not specified	Uncertain significance (Feb 23, 2023)
6-28575354-T-G		not specified	Uncertain significance (Oct 28, 2023)
6-28575396-C-G		not specified	Uncertain significance (Nov 15, 2024)
6-28575460-C-T		not specified	Likely benign (Dec 21, 2023)
6-28575510-G-C		not specified	Uncertain significance (Sep 25, 2023)
6-28575561-T-G		not specified	Uncertain significance (Dec 04, 2024)
6-28575566-A-G		not specified	Uncertain significance (Jul 27, 2024)
6-28575601-A-C		not specified	Uncertain significance (Jan 31, 2022)
6-28575630-G-A		not specified	Uncertain significance (Jun 26, 2024)
6-28575665-G-A		not specified	Uncertain significance (Nov 12, 2021)
6-28575731-C-T		not specified	Uncertain significance (Jun 07, 2023)
6-28575792-C-T		not specified	Uncertain significance (Jun 06, 2023)
6-28575810-G-A		not specified	Uncertain significance (Dec 28, 2022)
6-28575890-C-T		not specified	Uncertain significance (May 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCAND3	protein_coding	protein_coding	ENST00000452236	4	44583

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.99e-9	1.00	125514	1	233	125748	0.000931

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	495	669	0.740	0.0000333	8774
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00171	0.00171
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00637	0.00638
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000332	0.000325
Middle Eastern	0.00637	0.00638
South Asian	0.000425	0.000392
Other	0.000657	0.000652

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0942

Intolerance Scores

• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.32

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.355
• ghis: 0.501

Essentials

• essential_gene_gene_trap: N

Gene ontology

• Biological process: regulation of transcription, DNA-templated;DNA integration
• Molecular function: nucleic acid binding;DNA-binding transcription factor activity