ZSCAN31

protein-coding

zinc finger and SCAN domain containing 31, the group of Zinc fingers C2H2-type|SCAN domain containing

Gene summary

This gene encodes a protein containing multiple C2H2-type zinc finger motifs. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

Previous symbols:

ZNF310P
ZNF323

MANE transcript

NM_030899.5

Inheritance

—

ClinVar variants

U:38B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr6:28,324,693-28,356,271

External References & Databases

Ensembl (ENSG00000235109)

Transcript & Mutation Effects

hg38 • Region Span ~31.6 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 ZSCAN31 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 35

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030899.5. 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
missense			35 clinvar	2 clinvar		37
nonsense			1 clinvar			1
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	38	2	1	41

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 91 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030899.5	RefSeq	NP_112161.3	3	MANE Select
ENST00000344279.11	Ensembl	ENSP00000345339.6	3	MANE Select
NM_001135215.1	RefSeq	NP_001128687.1	3	Standard
NM_001135216.1	RefSeq	NP_001128688.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000414429
Coding exons: 3
Length: 31579
Individuals with no LoFs: 124074
Homozygous LoFs: 10
Heterozygous LoFs: 1664
Defined: 125748
p: 0.00668

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0842	209	212	0.984	0.0000114	2684
Missense (PolyPhen)		67	65.649	1.0206		848
Synonymous	-0.372	80	75.9	1.05	0.00000354	742
Loss of Function	1.07	14	19.0	0.736	0.00000132	191

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00098	0.00092	rare
Latino/Admixed American	0.011	0.011	notable
Ashkenazi Jewish	0.00060	0.00060	rare
East Asian	0.0029	0.0028	notable
Finnish	0.010	0.010	notable
European (Non-Finnish)	0.0069	0.0069	notable
South Asian	0.0056	0.0055	notable
Other	0.0056	0.0056	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function as a transcription factor. May be involved in the development of multiple embryonic organs.;

Intolerance Scores

RVIS EVS: 1
RVIS percentile EVS: 90.62

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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