ARMH1

protein-coding

armadillo like helical domain containing 1, the group of Armadillo like helical domain containing

Gene summary

Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

NCRNA00082
C1orf228

MANE transcript

NM_001145636.2

Inheritance

—

ClinVar variants

U:11B:3

Top phenotype

RNU5F-1-associated neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr1:44,674,692-44,725,591

External References & Databases

Ensembl (ENSG00000198520)

Transcript & Mutation Effects

hg38 • Region Span ~50.9 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 ARMH1 variants in ClinVar

3 Conditions Cataloged

not providedTotal: 6

not specifiedTotal: 5

RNU5F-1-associated neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001145636.2. 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			1 clinvar		1 clinvar	2
missense			8 clinvar	1 clinvar	1 clinvar	10
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	11	1	2	14

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001145636.2	RefSeq	NP_001139108.1	11	MANE Select
ENST00000535358.6	Ensembl	ENSP00000440524.1	11	MANE Select
ENST00000418644.5	Ensembl	ENSP00000417206.1	3	Standard
ENST00000434068.1	Ensembl	ENSP00000420050.1	5	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000458657
Coding exons: 11
Length: 50900
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	1.52	177	244	0.725	0.0000147	2853
Missense (PolyPhen)		72	84.601	0.85105		1090
Synonymous	2.01	79	105	0.750	0.00000722	856
Loss of Function	1.97	11	20.7	0.532	0.00000106	260

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

Intolerance Scores

RVIS EVS: 0.59
RVIS percentile EVS: 82.45