TMEM94

transmembrane protein 94, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 17:75441159-75500452

Previous symbols: [ "KIAA0195" ]

Links

ENSG00000177728 ∙ NCBI:9772 ∙ OMIM:618163 ∙ HGNC:28983 ∙ Uniprot:Q12767 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual developmental disorder with cardiac defects and dysmorphic facies (Supportive), mode of inheritance: AR
• intellectual developmental disorder with cardiac defects and dysmorphic facies (Moderate), mode of inheritance: AR
• intellectual developmental disorder with cardiac defects and dysmorphic facies (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder with cardiac defects and dysmorphic facies	AR	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic	30526868; 32825426

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMEM94 gene.

• Inborn_genetic_diseases (167 variants)
• not_provided (50 variants)
• Intellectual_developmental_disorder_with_cardiac_defects_and_dysmorphic_facies (34 variants)
• TMEM94-related_disorder (34 variants)
• not_specified (4 variants)
• Rare_syndromic_intellectual_disability (2 variants)
• Prostate_cancer (1 variants)
• Abnormality_of_the_nervous_system (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM94 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014738.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	27	1	29
missense			181	13	2	196
nonsense	3	3	1			7
start loss						0
frameshift	4	7	2			13
splice donor/acceptor (+/-2bp)	2	2				4
Total	9	12	185	40	3

Highest pathogenic variant AF is 0.000024784653

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM94	protein_coding	protein_coding	ENST00000314256	31	58932

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.75e-14	1.00	125652	0	96	125748	0.000382

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.50	619	821	0.754	0.0000507	8839
Missense in Polyphen		218	335.37	0.65002		3805
Synonymous	0.654	337	353	0.956	0.0000224	2769
Loss of Function	4.07	35	72.4	0.483	0.00000381	726

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00148	0.00148
Ashkenazi Jewish	0.000404	0.000397
East Asian	0.000328	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000383	0.000378
Middle Eastern	0.000328	0.000326
South Asian	0.000332	0.000327
Other	0.000175	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.132

Intolerance Scores

• rvis_EVS: -2.74
• rvis_percentile_EVS: 0.68

Haploinsufficiency Scores

• pHI: 0.475
• hipred: Y
• hipred_score: 0.575
• ghis: 0.665

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tmem94
• Phenotype: growth/size/body region phenotype; hematopoietic system phenotype

Gene ontology

• Cellular component: integral component of membrane