TMEM213

transmembrane protein 213

Basic information

Region (hg38): 7:138797952-138838101

Links

ENSG00000214128 ∙ NCBI:155006 ∙ ∙ HGNC:27220 ∙ Uniprot:A2RRL7 ∙ 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 TMEM213 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM213 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			9	3	1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			2		2	4
Total	0	0	13	3	3

Variants in TMEM213

This is a list of pathogenic ClinVar variants found in the TMEM213 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-138798048-C-T		Autosomal recessive distal renal tubular acidosis	Uncertain significance (Jan 12, 2018)
7-138798049-G-A		Autosomal recessive distal renal tubular acidosis	Uncertain significance (Jan 13, 2018)
7-138798050-G-A		Autosomal recessive distal renal tubular acidosis	Benign (Jan 12, 2018)
7-138798082-G-A		Autosomal recessive distal renal tubular acidosis	Benign (Jan 12, 2018)
7-138798112-G-A		Autosomal recessive distal renal tubular acidosis	Benign (Jan 13, 2018)
7-138798119-C-T		Autosomal recessive distal renal tubular acidosis	Uncertain significance (Jan 12, 2018)
7-138798120-G-T		not specified	Likely benign (Jan 29, 2024)
7-138798153-G-C		Autosomal recessive distal renal tubular acidosis	Uncertain significance (Jan 12, 2018)
7-138798161-C-T		Autosomal recessive distal renal tubular acidosis	Uncertain significance (Jan 13, 2018)
7-138798169-A-G		not specified	Uncertain significance (Mar 15, 2023)
7-138798172-C-T		not specified	Uncertain significance (Jun 03, 2022)
7-138798181-C-T		not specified	Likely benign (Aug 17, 2022)
7-138798194-T-C		Autosomal recessive distal renal tubular acidosis	Uncertain significance (Jan 12, 2018)
7-138801354-T-C		not specified	Uncertain significance (May 17, 2023)
7-138801359-G-A		not specified	Likely benign (May 02, 2024)
7-138802926-C-T		not specified	Uncertain significance (Sep 25, 2023)
7-138802927-G-A		not specified	Uncertain significance (Jun 10, 2022)
7-138802936-G-A		not specified	Likely benign (Dec 21, 2023)
7-138802945-T-G		not specified	Uncertain significance (Dec 16, 2022)
7-138802956-G-A		not specified	Uncertain significance (Oct 04, 2022)
7-138802974-G-A		not specified	Uncertain significance (Dec 12, 2022)
7-138837915-G-A			Likely benign (Aug 16, 2022)
7-138837918-G-C			Uncertain significance (Apr 21, 2022)
7-138837926-C-T		Inborn genetic diseases • Retinal dystrophy	Uncertain significance (Oct 01, 2023)
7-138837927-G-A			Likely benign (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM213	protein_coding	protein_coding	ENST00000442682	3	40152

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0867	0.773	123962	0	3	123965	0.0000121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.242	57	62.4	0.914	0.00000360	681
Missense in Polyphen		1	4.1589	0.24045		42
Synonymous	-0.0283	28	27.8	1.01	0.00000172	218
Loss of Function	1.10	2	4.52	0.443	1.94e-7	47

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	0.0000982	0.0000981
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.401
• rvis_EVS: 0.41
• rvis_percentile_EVS: 76.67

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.223

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem213

Gene ontology

• Cellular component: integral component of membrane