AMMECR1

AMMECR nuclear protein 1, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): X:110194186-110440318

Links

ENSG00000101935 ∙ NCBI:9949 ∙ OMIM:300195 ∙ HGNC:467 ∙ Uniprot:Q9Y4X0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis (Strong), mode of inheritance: XL
• midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis (Moderate), mode of inheritance: XL
• Alport syndrome-intellectual disability-midface hypoplasia-elliptocytosis syndrome (Supportive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis	XL	Hematologic	Ellipsocytosis requiring red blood cell transfusion has been described, and awareness may allow early diagnosis and management	Audiologic/Otolaryngologic; Craniofacial; Hematologic; Musculoskeletal; Renal	27811305; 28089922

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AMMECR1 gene.

• not_provided (35 variants)
• not_specified (31 variants)
• Midface_hypoplasia,_hearing_impairment,_elliptocytosis,_and_nephrocalcinosis (10 variants)
• AMMECR1-related_disorder (4 variants)
• Skraban-Deardorff_syndrome (1 variants)
• Nephrocalcinosis (1 variants)
• Short_stature (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMMECR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015365.3. 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				6	2	8
missense	1		45	5		51
nonsense		5	3			8
start loss						0
frameshift	2	2	1			5
splice donor/acceptor (+/-2bp)		2				2
Total	3	9	49	11	2

Highest pathogenic variant AF is 0.000001854075

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMMECR1	protein_coding	protein_coding	ENST00000262844	6	246048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.821	0.178	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	90	124	0.727	0.00000918	2095
Missense in Polyphen		19	45.226	0.42011		736
Synonymous	0.273	47	49.4	0.951	0.00000353	710
Loss of Function	2.64	1	10.0	0.0995	6.96e-7	187

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	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis (MFHIEN) [MIM:300990]: An X-linked recessive disorder with onset in early childhood, characterized by midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis. Variable clinical features include anemia, and mild early motor or speech delay. {ECO:0000269|PubMed:27811305, ECO:0000269|PubMed:28089922}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Alport syndrome with mental retardation, midface hypoplasia and elliptocytosis (ATS-MR) [MIM:300194]: A X-linked contiguous gene deletion syndrome characterized by glomerulonephritis, sensorineural hearing loss, mental retardation, midface hypoplasia and elliptocytosis. {ECO:0000269|PubMed:10049589}. Note=The gene represented in this entry may be involved in disease pathogenesis.

Recessive Scores

• pRec: 0.338

Intolerance Scores

• loftool: 0.0853
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.896
• hipred: Y
• hipred_score: 0.662
• ghis: 0.652

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ammecr1

Zebrafish Information Network

• Gene name: ammecr1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: kinked

Gene ontology

• Biological process: biological_process
• Cellular component: nucleus
• Molecular function: protein binding