ZNF638

zinc finger protein 638, the group of RNA binding motif containing

Basic information

Region (hg38): 2:71276560-71435069

Previous symbols: [ "ZFML" ]

Links

ENSG00000075292 ∙ NCBI:27332 ∙ OMIM:614349 ∙ HGNC:17894 ∙ Uniprot:Q14966 ∙ 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 ZNF638 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF638 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				1	4	5
missense			92	11		103
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	92	12	4

Variants in ZNF638

This is a list of pathogenic ClinVar variants found in the ZNF638 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-71349053-G-T		not specified	Uncertain significance (May 13, 2024)
2-71349108-C-T		not specified	Uncertain significance (Aug 26, 2022)
2-71349168-C-G		not specified	Uncertain significance (Jul 21, 2021)
2-71349171-G-A		not specified	Uncertain significance (Apr 29, 2024)
2-71349243-G-C		not specified	Uncertain significance (Apr 13, 2023)
2-71349300-G-A		not specified	Uncertain significance (Apr 24, 2024)
2-71349343-A-G		not specified	Uncertain significance (Dec 19, 2023)
2-71349355-G-A		not specified	Uncertain significance (Apr 04, 2023)
2-71349429-C-T		not specified	Uncertain significance (Jan 17, 2024)
2-71349433-A-T		not specified	Uncertain significance (Jul 12, 2023)
2-71349508-G-A		not specified	Uncertain significance (Jun 05, 2023)
2-71349549-C-T		not specified	Uncertain significance (Jan 04, 2022)
2-71349552-G-A		not specified	Uncertain significance (Dec 28, 2023)
2-71349661-A-T		not specified	Uncertain significance (Jan 24, 2024)
2-71349669-G-A		not specified	Likely benign (Dec 03, 2021)
2-71349691-A-G		not specified	Uncertain significance (May 08, 2024)
2-71349750-G-A		not specified	Uncertain significance (Feb 27, 2024)
2-71349792-A-G		not specified	Uncertain significance (Feb 13, 2024)
2-71349793-A-G		not specified	Uncertain significance (Apr 08, 2024)
2-71349799-G-A		not specified	Likely benign (Dec 08, 2023)
2-71349817-A-G		not specified	Uncertain significance (May 25, 2022)
2-71349882-T-A		not specified	Uncertain significance (Dec 12, 2023)
2-71349885-G-A		not specified	Uncertain significance (Jan 18, 2022)
2-71349889-A-G		not specified	Likely benign (Aug 11, 2022)
2-71349921-A-G		not specified	Uncertain significance (Jun 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF638	protein_coding	protein_coding	ENST00000409544	27	158509

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.19e-8	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.575	1060	1.01e+3	1.05	0.0000507	13049
Missense in Polyphen		258	298.35	0.86475		3968
Synonymous	-1.21	371	342	1.08	0.0000171	3708
Loss of Function	7.77	8	85.6	0.0934	0.00000466	1178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000800	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Early regulator of adipogenesis that works as a transcription cofactor of CEBPs, controlling the expression of PPARG and probably of other proadipogenic genes, such as SREBF1 (By similarity). Binds to cytidine clusters in double-stranded DNA (PubMed:8647861). May also regulate alternative splicing of target genes during adipogenesis (By similarity). {ECO:0000250|UniProtKB:Q61464, ECO:0000269|PubMed:8647861}.

Recessive Scores

• pRec: 0.0937

Intolerance Scores

• loftool: 0.439
• rvis_EVS: -1.6
• rvis_percentile_EVS: 3.02

Haploinsufficiency Scores

• pHI: 0.531
• hipred: Y
• hipred_score: 0.701
• ghis: 0.645

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.559

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp638

Gene ontology

• Biological process: RNA splicing
• Cellular component: nucleoplasm;cytoplasm;nuclear speck;intracellular membrane-bounded organelle
• Molecular function: double-stranded DNA binding;RNA binding;zinc ion binding