CWH43

protein-coding

cell wall biogenesis 43 C-terminal homolog

Gene summary

Predicted to be involved in GPI anchor biosynthetic process. Predicted to act upstream of or within several processes, including cerebrospinal fluid circulation; membrane protein ectodomain proteolysis; and protein import into nucleus. Predicted to be located in membrane. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_025087.3

Inheritance

—

ClinVar variants

U:94B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr4:48,986,275-49,062,081

External References & Databases

Ensembl (ENSG00000109182)

Transcript & Mutation Effects

hg38 • Region Span ~75.8 kb

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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 CWH43 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 95

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025087.3. 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			2 clinvar			2
missense			92 clinvar	4 clinvar	3 clinvar	99
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	94	5	3	102

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025087.3	RefSeq	NP_079363.2	16	MANE Select
ENST00000226432.9	Ensembl	ENSP00000226432.4	16	MANE Select
NM_001286791.2	RefSeq	NP_001273720.1	15	Standard
ENST00000513409.1	Ensembl	ENSP00000422802.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

GPI anchor biosynthetic process

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000226432
Coding exons: 16
Length: 75835
Individuals with no LoFs: 122100
Homozygous LoFs: 42
Heterozygous LoFs: 3606
Defined: 125748
p: 0.0146

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0595	368	365	1.01	0.0000174	4533
Missense (PolyPhen)		117	123.4	0.94813		1528
Synonymous	-2.27	164	131	1.25	0.00000651	1360
Loss of Function	0.397	34	36.6	0.929	0.00000169	441

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0056	0.0056	notable
Latino/Admixed American	0.010	0.010	notable
Ashkenazi Jewish	0.0087	0.0086	notable
East Asian	0.012	0.012	notable
Finnish	0.011	0.011	notable
European (Non-Finnish)	0.020	0.020	notable
South Asian	0.011	0.011	notable
Other	0.018	0.018	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in lipid remodeling during GPI-anchor maturation. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.826
RVIS EVS: 0.02
RVIS percentile EVS: 55.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0737

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High