ZNRD2

zinc ribbon domain containing 2

Basic information

Region (hg38): 11:65570459-65573942

Previous symbols: [ "SSSCA1" ]

Links

ENSG00000173465 ∙ NCBI:10534 ∙ OMIM:606044 ∙ HGNC:11328 ∙ Uniprot:O60232 ∙ 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 ZNRD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNRD2 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						0
missense			8		1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	8	0	2

Variants in ZNRD2

This is a list of pathogenic ClinVar variants found in the ZNRD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65570495-G-T		not specified	Uncertain significance (Nov 07, 2022)
11-65570504-G-A		not specified	Uncertain significance (Feb 16, 2023)
11-65570520-T-C			Benign (Feb 25, 2018)
11-65570646-C-T			Benign (Dec 31, 2019)
11-65571396-A-C		not specified	Uncertain significance (Nov 21, 2023)
11-65571496-G-T		not specified	Uncertain significance (Apr 12, 2023)
11-65571504-C-T		not specified	Uncertain significance (Apr 12, 2023)
11-65571538-C-T		not specified	Uncertain significance (Sep 14, 2023)
11-65571558-G-C		not specified	Uncertain significance (Oct 25, 2022)
11-65571633-G-C		not specified	Uncertain significance (Jun 16, 2024)
11-65571712-G-T		not specified	Uncertain significance (Oct 26, 2022)
11-65572676-G-A		not specified	Uncertain significance (Aug 08, 2022)
11-65572772-G-T		not specified	Uncertain significance (Jun 24, 2022)
11-65572874-G-T		not specified	Uncertain significance (Jan 26, 2023)
11-65572881-C-T		not specified	Uncertain significance (Jul 14, 2021)
11-65572902-C-T		not specified	Uncertain significance (Mar 08, 2024)
11-65572916-C-T		not specified	Uncertain significance (Jun 09, 2022)
11-65573462-T-C		not specified	Uncertain significance (May 04, 2023)
11-65573479-C-T		not specified	Likely benign (Mar 01, 2024)
11-65573515-G-A		not specified	Likely benign (Jun 21, 2023)
11-65573543-G-A		not specified	Uncertain significance (Jun 21, 2022)
11-65573604-A-C		not specified	Uncertain significance (Oct 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNRD2	protein_coding	protein_coding	ENST00000309328	4	3513

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.84e-7	0.140	125722	0	16	125738	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.600	103	122	0.847	0.00000636	1253
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000443	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.000263	0.000261
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.211
• hipred: N
• hipred_score: 0.397
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.938

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sssca1

Gene ontology

• Biological process: mitotic cell cycle;cell division
• Molecular function: protein binding;identical protein binding