TMEFF1

transmembrane protein with EGF like and two follistatin like domains 1

Basic information

Region (hg38): 9:100473149-100577636

Previous symbols: [ "C9orf2" ]

Links

ENSG00000241697 ∙ NCBI:8577 ∙ OMIM:603421 ∙ HGNC:11866 ∙ Uniprot:Q8IYR6 ∙ 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 TMEFF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEFF1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in TMEFF1

This is a list of pathogenic ClinVar variants found in the TMEFF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-100473554-G-A		not specified	Uncertain significance (Jul 19, 2022)
9-100473555-C-T		not specified	Uncertain significance (Jan 02, 2024)
9-100473630-T-A		not specified	Uncertain significance (Jul 06, 2021)
9-100473671-C-T		not specified	Uncertain significance (Jan 29, 2024)
9-100473707-C-T		not specified	Uncertain significance (Mar 28, 2024)
9-100473724-G-C		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEFF1	protein_coding	protein_coding	ENST00000374879	10	135359

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.538	0.462	125687	0	18	125705	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	148	191	0.776	0.00000881	2464
Missense in Polyphen		50	75.771	0.65988		958
Synonymous	0.533	61	66.5	0.917	0.00000315	694
Loss of Function	3.26	4	19.6	0.204	9.52e-7	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000125
Ashkenazi Jewish	0.000602	0.000596
East Asian	0.0000549	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000714	0.0000704
Middle Eastern	0.0000549	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May inhibit NODAL and BMP signaling during neural patterning (By similarity). May be a tumor suppressor in brain cancers. {ECO:0000250, ECO:0000269|PubMed:12743596}.

Recessive Scores

• pRec: 0.347

Intolerance Scores

• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.293
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.241

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmeff1

Gene ontology

• Biological process: multicellular organism development
• Cellular component: plasma membrane;integral component of membrane