NUFIP1

nuclear FMR1 interacting protein 1

Basic information

Region (hg38): 13:44939249-44989471

Links

ENSG00000083635 ∙ NCBI:26747 ∙ OMIM:604354 ∙ HGNC:8057 ∙ Uniprot:Q9UHK0 ∙ 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 NUFIP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUFIP1 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				4	3	7
missense			46	2	2	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	6	5

Variants in NUFIP1

This is a list of pathogenic ClinVar variants found in the NUFIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-44941224-C-T			Benign (Dec 31, 2019)
13-44943477-C-T		not specified	Uncertain significance (Jan 29, 2024)
13-44943488-T-C		not specified	Uncertain significance (Dec 21, 2021)
13-44943520-G-T		not specified	Uncertain significance (Jun 17, 2024)
13-44943540-T-G		not specified	Uncertain significance (Mar 11, 2024)
13-44943545-C-T		not specified	Likely benign (Jun 24, 2022)
13-44943546-G-C		not specified	Uncertain significance (Dec 21, 2022)
13-44943572-T-C		not specified	Uncertain significance (Dec 21, 2022)
13-44943609-T-C		not specified	Uncertain significance (Feb 28, 2024)
13-44943622-A-T			Benign (Dec 31, 2019)
13-44943664-G-C		not specified	Uncertain significance (Mar 01, 2023)
13-44943666-T-C		not specified	Uncertain significance (Jan 18, 2023)
13-44943667-G-A			Likely benign (May 14, 2018)
13-44949785-G-A		not specified	Uncertain significance (Mar 25, 2024)
13-44959388-A-T		not specified	Uncertain significance (Oct 09, 2024)
13-44959389-C-T		not specified	Uncertain significance (Dec 10, 2024)
13-44959414-C-G		not specified	Uncertain significance (Sep 11, 2024)
13-44959428-G-A		not specified	Uncertain significance (Dec 22, 2023)
13-44959474-T-C		not specified	Uncertain significance (Feb 16, 2023)
13-44959482-C-G		not specified	Uncertain significance (Dec 01, 2022)
13-44959492-A-T		not specified	Uncertain significance (Jan 06, 2023)
13-44959559-C-T		not specified	Uncertain significance (Dec 03, 2021)
13-44959561-T-A		not specified	Uncertain significance (Dec 18, 2023)
13-44965857-T-C		not specified	Uncertain significance (May 26, 2023)
13-44965931-T-A		not specified	Uncertain significance (Dec 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUFIP1	protein_coding	protein_coding	ENST00000379161	10	50235

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.29e-8	0.881	125671	0	76	125747	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.168	268	260	1.03	0.0000126	3271
Missense in Polyphen		72	77.112	0.9337		974
Synonymous	-1.24	110	94.6	1.16	0.00000487	899
Loss of Function	1.66	15	23.7	0.633	0.00000115	306

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.00101
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.0000562	0.0000544
Finnish	0.000280	0.000277
European (Non-Finnish)	0.000286	0.000281
Middle Eastern	0.0000562	0.0000544
South Asian	0.000110	0.0000980
Other	0.000878	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds RNA. {ECO:0000269|PubMed:10556305}.

Intolerance Scores

• loftool: 0.821
• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.11

Haploinsufficiency Scores

• pHI: 0.553
• hipred: N
• hipred_score: 0.352
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.635

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nufip1

Gene ontology

• Biological process: box C/D snoRNP assembly;RNA processing;positive regulation of transcription by RNA polymerase II;protein complex oligomerization
• Cellular component: fibrillar center;nucleus;perichromatin fibrils;nucleolus;transcription elongation factor complex;nuclear matrix;cytosolic ribosome;protein-containing complex;presynaptic active zone;pre-snoRNP complex
• Molecular function: DNA binding;RNA binding;protein binding;snoRNA binding;protein binding, bridging;identical protein binding;metal ion binding;ATPase binding