TMEM47

transmembrane protein 47

Basic information

Region (hg38): X:34627075-34657285

Previous symbols: [ "TM4SF10" ]

Links

ENSG00000147027 ∙ NCBI:83604 ∙ OMIM:300698 ∙ HGNC:18515 ∙ Uniprot:Q9BQJ4 ∙ 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 TMEM47 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM47 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				2		2
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	2	0

Variants in TMEM47

This is a list of pathogenic ClinVar variants found in the TMEM47 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-34630363-C-A		not specified	Uncertain significance (May 20, 2024)
X-34639271-C-T		not specified	Uncertain significance (Oct 25, 2023)
X-34656811-G-A			Likely benign (Oct 09, 2018)
X-34656847-G-A			Likely benign (May 24, 2018)
X-34656995-C-G		6 conditions	Likely pathogenic (Jan 10, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM47	protein_coding	protein_coding	ENST00000275954	3	30225

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.797	0.198	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	41	63.7	0.644	0.00000452	1141
Missense in Polyphen		24	28.377	0.84575		487
Synonymous	-1.23	36	27.7	1.30	0.00000200	376
Loss of Function	2.13	0	5.27	0.00	3.87e-7	83

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates cell junction organization in epithelial cells. May play a role in the transition from adherens junction to tight junction assembly. May regulate F-actin polymerization required for tight junctional localization dynamics and affect the junctional localization of PARD6B. During podocyte differentiation may negatively regulate activity of FYN and subsequently the abundance of nephrin (By similarity). {ECO:0000250|UniProtKB:Q9JJG6, ECO:0000250|UniProtKB:Q9XSV3}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.404
• hipred: N
• hipred_score: 0.418
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem47

Gene ontology

• Biological process: biological_process
• Cellular component: plasma membrane;cell-cell junction;adherens junction;integral component of membrane;cell junction
• Molecular function: molecular_function