ZNRD2

protein-coding

zinc ribbon domain containing 2

Gene summary

This antigen is recognized by a subset of anti-centromere antibodies from patients with scleroderma and/or Sjogren's syndrome. Subcellular localization has not yet been established. [provided by RefSeq, Jul 2008]

Previous symbols:

SSSCA1

MANE transcript

NM_006396.3

Inheritance

—

ClinVar variants

U:26B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.06

Max pathogenic AF

—

Genomic locus

chr11:65,570,460-65,573,942

External References & Databases

Ensembl (ENSG00000173465)

Transcript & Mutation Effects

hg38 • Region Span ~3.5 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 ZNRD2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 26

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006396.3. 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			26 clinvar		1 clinvar	27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	26	0	1	27

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006396.3	RefSeq	NP_006387.1	4	MANE Select
ENST00000309328.8	Ensembl	ENSP00000312318.3	4	MANE Select
NM_001303024.2	RefSeq	NP_001289953.1	3	Standard
ENST00000526433.1	Ensembl	ENSP00000435982.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mitotic cell cycle
cell division

Molecular Function

protein binding
identical protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000309328
Coding exons: 4
Length: 3513
Individuals with no LoFs: 125722
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125738
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.600	103	122	0.847	0.00000636	1253
Missense (PolyPhen)		39	46.66	0.83584		510
Synonymous	1.20	41	52.0	0.789	0.00000265	435
Loss of Function	-0.172	10	9.43	1.06	4.68e-7	94

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.00026	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Might play a role in mitosis. Antigenic molecule. Could be a centromere-associated protein. May induce anti-centromere antibodies.;

Recessive Scores

pRec: 0.177

Intolerance Scores

LoFtool: 0.676
RVIS EVS: 0.04
RVIS percentile EVS: 56.64

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.938

Gene Damage Prediction

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