NYNRIN

NYN domain and retroviral integrase containing

Basic information

Region (hg38): 14:24399002-24419283

Previous symbols: [ "KIAA1305" ]

Links

ENSG00000205978 ∙ NCBI:57523 ∙ OMIM:620129 ∙ HGNC:20165 ∙ Uniprot:Q9P2P1 ∙ 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 NYNRIN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NYNRIN 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			7	16	8	31
missense			106	13	5	124
nonsense						0
start loss						0
frameshift			1			1
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				1	3	4
non coding				1	3	4
Total	0	0	114	30	17

Variants in NYNRIN

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

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

Position	Type	Phenotype	Significance	ClinVar
14-24399254-T-C		not specified	Uncertain significance (Apr 04, 2024)
14-24399331-C-T			Likely benign (Dec 24, 2023)
14-24399394-T-C		not specified	Uncertain significance (Jul 13, 2022)
14-24399431-T-C		not specified	Likely benign (Jan 16, 2024)
14-24407856-C-T			Benign (Jan 25, 2024)
14-24407858-A-G			Benign (Feb 01, 2024)
14-24407864-C-T			Benign (Jan 18, 2024)
14-24407873-A-G		not specified	Uncertain significance (Aug 14, 2023)
14-24407914-C-T		not specified	Uncertain significance (Dec 09, 2023)
14-24407955-A-G			Benign (Feb 01, 2024)
14-24408009-C-T			Benign (Dec 27, 2023)
14-24408013-C-G		not specified	Uncertain significance (Jun 09, 2022)
14-24408033-C-T			Benign (Jan 06, 2024)
14-24408145-G-T		not specified	Uncertain significance (Sep 14, 2021)
14-24408221-C-A		NYNRIN-related disorder	Uncertain significance (Dec 14, 2022)
14-24408262-G-A		not specified	Uncertain significance (Mar 12, 2024)
14-24408293-G-A		not specified	Likely benign (Mar 17, 2023)
14-24408299-G-C		not specified	Uncertain significance (Apr 07, 2022)
14-24408323-C-T		not specified	Uncertain significance (Apr 06, 2024)
14-24408341-C-T		not specified	Uncertain significance (Jul 12, 2022)
14-24408368-C-T		not specified	Uncertain significance (Apr 23, 2024)
14-24408403-G-A		not specified	Uncertain significance (Oct 05, 2023)
14-24408460-C-T			Uncertain significance (Jan 20, 2024)
14-24408493-A-G			Benign (Jan 31, 2024)
14-24408518-A-G			Uncertain significance (Jan 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NYNRIN	protein_coding	protein_coding	ENST00000382554	8	20503

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.48e-9	1.00	124903	0	70	124973	0.000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	911	1.05e+3	0.864	0.0000585	12184
Missense in Polyphen		292	407.18	0.71713		4714
Synonymous	-0.337	470	461	1.02	0.0000267	4080
Loss of Function	4.47	27	66.3	0.408	0.00000353	674

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000689	0.000675
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000221
Finnish	0.000193	0.000186
European (Non-Finnish)	0.000350	0.000345
Middle Eastern	0.000223	0.000221
South Asian	0.000164	0.000163
Other	0.000504	0.000493

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0970

Intolerance Scores

• loftool: 0.688
• rvis_EVS: -1.01
• rvis_percentile_EVS: 8.22

Haploinsufficiency Scores

• pHI: 0.207
• hipred: N
• hipred_score: 0.379
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nynrin

Gene ontology

• Biological process: biological_process;DNA integration
• Cellular component: cellular_component;integral component of membrane
• Molecular function: molecular_function;nucleic acid binding