ZFTRAF1

zinc finger TRAF-type containing 1, the group of Ring finger proteins|Zinc fingers TRAF-type

Basic information

Region (hg38): 8:144449582-144462871

Previous symbols: [ "CYHR1" ]

Links

ENSG00000187954 ∙ NCBI:50626 ∙ OMIM:616635 ∙ HGNC:17806 ∙ Uniprot:P0DTL6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR
• neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZFTRAF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFTRAF1 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in ZFTRAF1

This is a list of pathogenic ClinVar variants found in the ZFTRAF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-144450430-CAG-C		Neurodevelopmental disorder with hypotonia and gross motor and speech delay	Likely pathogenic (-)
8-144450507-CAA-C		Neurodevelopmental disorder with hypotonia and gross motor and speech delay	Pathogenic (-)
8-144452428-G-A		not specified	Uncertain significance (Mar 06, 2023)
8-144452572-T-G		Neurodevelopmental disorder with hypotonia and gross motor and speech delay	Pathogenic (-)
8-144453277-G-A		not specified	Uncertain significance (Feb 16, 2023)
8-144453351-T-C		not specified	Uncertain significance (Oct 06, 2024)
8-144453385-C-T		not specified	Uncertain significance (Jul 16, 2024)
8-144453422-G-C		not specified	Uncertain significance (Mar 18, 2024)
8-144453426-A-G		not specified	Uncertain significance (Apr 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFTRAF1	protein_coding	protein_coding	ENST00000438911	5	16096

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.491	0.508	125432	0	12	125444	0.0000478

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.15	96	231	0.416	0.0000148	2348
Missense in Polyphen		16	88.282	0.18124		834
Synonymous	0.286	105	109	0.965	0.00000812	736
Loss of Function	2.83	3	14.7	0.204	7.37e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000201	0.000199
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000536	0.0000529
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.767
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.439
• ghis: 0.601

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.473

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyhr1

Gene ontology

• Cellular component: nucleoplasm;perinuclear region of cytoplasm
• Molecular function: protein binding;zinc ion binding