TMEM47

protein-coding

transmembrane protein 47

Gene summary

This gene encodes a member of the PMP22/EMP/claudin protein family. The encoded protein is localized to the ER and the plasma membrane. In dogs, transcripts of this gene exist at high levels in the brain. [provided by RefSeq, Jul 2008]

Previous symbols:

TM4SF10

MANE transcript

NM_031442.4

Inheritance

—

ClinVar variants

P:1U:22B:2

Top phenotype

Hypoplasia of the corpus callosum

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:34,627,075-34,657,285

External References & Databases

Ensembl (ENSG00000147027)

Transcript & Mutation Effects

hg38 • Region Span ~30.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMEM47 variants in ClinVar

8 Conditions Cataloged

not specifiedTotal: 10

not providedTotal: 2

Hypoplasia of the corpus callosumTotal: 1

HypotoniaTotal: 1

Global developmental delayTotal: 1

Attention deficit hyperactivity disorderTotal: 1

Dandy-Walker syndromeTotal: 1

Cerebellar atrophyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031442.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	2 clinvar		8
missense		1 clinvar	16 clinvar			17
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	22	2	0	25

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031442.4	RefSeq	NP_113630.1	3	MANE Select
ENST00000275954.4	Ensembl	ENSP00000275954.3	3	MANE Select
ENST00000876538.1	Ensembl	ENSP00000546597.1	2	Standard
ENST00000876538.2	Ensembl	ENSP00000546597.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

plasma membrane
cell-cell junction
adherens junction
integral component of membrane
cell junction

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000275954
Coding exons: 3
Length: 30225
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.01	41	63.7	0.644	0.00000452	1141
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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