SPDEF

SAM pointed domain containing ETS transcription factor, the group of ETS transcription factor family

Basic information

Region (hg38): 6:34537802-34556333

Links

ENSG00000124664 ∙ NCBI:25803 ∙ OMIM:608144 ∙ HGNC:17257 ∙ Uniprot:O95238 ∙ 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 SPDEF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPDEF 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	2	3
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	2

Variants in SPDEF

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

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

Position	Type	Phenotype	Significance	ClinVar
6-34538363-G-T		not specified	Uncertain significance (Sep 30, 2021)
6-34538376-G-A			Likely benign (Nov 01, 2022)
6-34538393-G-A		not specified	Uncertain significance (Dec 19, 2023)
6-34538417-G-A		not specified	Uncertain significance (Jan 11, 2023)
6-34539300-A-T		not specified	Uncertain significance (Apr 06, 2023)
6-34539523-T-C		not specified	Uncertain significance (Jul 07, 2024)
6-34539533-C-T		not specified	Uncertain significance (Dec 26, 2023)
6-34539538-G-A		not specified	Uncertain significance (Dec 20, 2023)
6-34539544-C-T		not specified	Uncertain significance (Jun 19, 2024)
6-34539545-G-A		not specified	Uncertain significance (Feb 21, 2024)
6-34541037-C-A		not specified	Uncertain significance (Feb 23, 2023)
6-34541058-G-A		not specified	Uncertain significance (Jan 29, 2024)
6-34541065-C-T		not specified	Uncertain significance (Mar 06, 2025)
6-34541082-G-A		not specified	Uncertain significance (Aug 05, 2024)
6-34541110-G-C		not specified	Uncertain significance (Jun 30, 2023)
6-34541114-C-G			Benign (May 21, 2018)
6-34544029-T-C		not specified	Uncertain significance (Aug 29, 2022)
6-34544128-C-T		not specified	Uncertain significance (Oct 26, 2022)
6-34544175-G-A		not specified	Uncertain significance (Dec 17, 2023)
6-34544196-G-A		not specified	Uncertain significance (Nov 13, 2024)
6-34544209-G-A		not specified	Uncertain significance (Oct 16, 2023)
6-34544223-G-A		not specified	Uncertain significance (Oct 12, 2024)
6-34544224-G-A		not specified	Uncertain significance (May 28, 2024)
6-34544227-C-A		not specified	Uncertain significance (Oct 14, 2021)
6-34544242-T-C		not specified	Uncertain significance (Jun 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPDEF	protein_coding	protein_coding	ENST00000374037	5	18532

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.972	0.0282	125344	0	3	125347	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.797	186	219	0.849	0.0000146	2160
Missense in Polyphen		56	83.137	0.67359		818
Synonymous	0.0982	97	98.2	0.987	0.00000708	656
Loss of Function	3.40	1	15.4	0.0648	6.61e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000704	0.0000618
Ashkenazi Jewish	0.000107	0.0000994
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000885	0.00000883
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as an androgen-independent transactivator of the prostate-specific antigen (PSA) promoter. Binds to 5'-GGAT- 3' DNA sequences. May play a role in the regulation of the prostate gland and/or prostate cancer development. Acts as a transcriptional activator for SERPINB5 promoter. {ECO:0000269|PubMed:10625666}.
• Pathway: AndrogenReceptor;Regulation of Androgen receptor activity (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.228
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.66

Haploinsufficiency Scores

• pHI: 0.169
• hipred: Y
• hipred_score: 0.644
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.978

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spdef
• Phenotype: respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; immune system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;multicellular organism development;negative regulation of cell fate commitment;positive regulation of cell fate commitment;cell differentiation;positive regulation of apoptotic process;positive regulation of transcription by RNA polymerase II;lung goblet cell differentiation;intestinal epithelial cell development
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;sequence-specific DNA binding