VEPH1

ventricular zone expressed PH domain containing 1, the group of Armadillo like helical domain containing|Pleckstrin homology domain containing

Basic information

Region (hg38): 3:157259741-157533619

Links

ENSG00000197415 ∙ NCBI:79674 ∙ OMIM:609594 ∙ HGNC:25735 ∙ Uniprot:Q14D04 ∙ 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 VEPH1 gene.

• Inborn genetic diseases (38 variants)
• not provided (6 variants)
• PTX3-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VEPH1 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			15		5	20
Total	0	0	39	1	5

Variants in VEPH1

This is a list of pathogenic ClinVar variants found in the VEPH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-157265531-T-G		not specified	Uncertain significance (Sep 12, 2023)
3-157265575-C-T		not specified	Uncertain significance (Feb 17, 2023)
3-157265592-G-C		not specified	Uncertain significance (Jan 18, 2022)
3-157265606-T-C		not specified	Uncertain significance (May 31, 2023)
3-157265642-G-A		not specified	Uncertain significance (Feb 28, 2024)
3-157286576-G-T		not specified	Uncertain significance (Dec 28, 2022)
3-157286626-C-T		not specified	Uncertain significance (Jun 18, 2021)
3-157317076-A-G		not specified	Uncertain significance (Sep 17, 2021)
3-157317132-C-T		not specified	Uncertain significance (Jul 09, 2021)
3-157363414-G-A		not specified	Uncertain significance (Sep 25, 2023)
3-157363478-T-C		not specified	Likely benign (Oct 26, 2021)
3-157363489-G-A		not specified	Uncertain significance (Dec 18, 2023)
3-157363622-G-A		not specified	Uncertain significance (Feb 05, 2024)
3-157363706-C-T		not specified	Uncertain significance (Sep 28, 2022)
3-157363721-C-T		Inborn genetic diseases	Uncertain significance (Feb 11, 2022)
3-157364373-G-C		not specified	Uncertain significance (Mar 28, 2023)
3-157364423-T-A		not specified	Uncertain significance (Feb 28, 2024)
3-157364456-A-G		not specified	Likely benign (Feb 02, 2024)
3-157381223-T-C		not specified	Uncertain significance (Feb 03, 2022)
3-157381236-G-C		not specified	Uncertain significance (Jul 13, 2021)
3-157414030-T-A		not specified	Uncertain significance (Aug 02, 2021)
3-157414046-A-T		not specified	Uncertain significance (Mar 31, 2022)
3-157414079-C-A		not specified	Uncertain significance (Jun 01, 2023)
3-157428324-C-T		not specified	Uncertain significance (May 11, 2022)
3-157436979-T-C			Benign (Jul 19, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VEPH1	protein_coding	protein_coding	ENST00000362010	13	273878

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.30e-22	0.00324	125624	0	124	125748	0.000493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.213	446	434	1.03	0.0000210	5535
Missense in Polyphen		145	133.47	1.0864		1762
Synonymous	1.15	142	161	0.884	0.00000847	1550
Loss of Function	0.449	35	38.0	0.921	0.00000188	465

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000623	0.000623
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000715	0.000712
Middle Eastern	0.000327	0.000326
South Asian	0.000425	0.000392
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interacts with TGF-beta receptor type-1 (TGFBR1) and inhibits dissociation of activated SMAD2 from TGFBR1, impeding its nuclear accumulation and resulting in impaired TGF-beta signaling. May also affect FOXO, Hippo and Wnt signaling. {ECO:0000269|PubMed:26039994}.

Recessive Scores

• pRec: 0.0970

Intolerance Scores

• loftool: 0.961
• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.69

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.455
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.305

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Veph1
• Phenotype: normal phenotype

Gene ontology

• Cellular component: plasma membrane
• Molecular function: protein binding