ZNF449

zinc finger protein 449, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): X:135344795-135363413

Links

ENSG00000173275 ∙ NCBI:203523 ∙ OMIM:300627 ∙ HGNC:21039 ∙ Uniprot:Q6P9G9 ∙ 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 ZNF449 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF449 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in ZNF449

This is a list of pathogenic ClinVar variants found in the ZNF449 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-135349117-T-C		not specified	Uncertain significance (Jul 19, 2023)
X-135349144-C-A		not specified	Uncertain significance (Jun 29, 2023)
X-135349149-G-A		Short stature	Uncertain significance (Nov 18, 2001)
X-135349185-G-C		not specified	Uncertain significance (Jan 23, 2024)
X-135349264-C-T		not specified	Uncertain significance (Jan 10, 2022)
X-135349306-T-A		not specified	Uncertain significance (Feb 26, 2024)
X-135359991-T-C		Short stature	Uncertain significance (Nov 18, 2001)
X-135360308-A-T		not specified	Uncertain significance (Jun 29, 2022)
X-135360339-G-A		not specified	Uncertain significance (Dec 21, 2023)
X-135360366-G-C		not specified	Uncertain significance (May 05, 2023)
X-135360418-A-G			Likely benign (Apr 01, 2023)
X-135360458-C-A		not specified	Uncertain significance (Aug 12, 2021)
X-135360795-C-G		not specified	Uncertain significance (Jun 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF449	protein_coding	protein_coding	ENST00000339249	4	18357

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.670	0.330	125521	0	4	125525	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.33	100	190	0.525	0.0000137	3412
Missense in Polyphen		17	55.962	0.30378		1068
Synonymous	0.579	60	66.0	0.909	0.00000461	955
Loss of Function	3.10	3	16.7	0.180	0.00000134	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000763	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000627	0.0000462
European (Non-Finnish)	0.0000124	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.0000562	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.428
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.36

Haploinsufficiency Scores

• pHI: 0.362
• hipred: Y
• hipred_score: 0.572
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp449

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;spermatogonial cell division
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding