AHNAK2

AHNAK nucleoprotein 2, the group of PDZ domain containing

Basic information

Region (hg38): 14:104937244-104978374

Previous symbols: [ "C14orf78" ]

Links

ENSG00000185567 ∙ NCBI:113146 ∙ OMIM:608570 ∙ HGNC:20125 ∙ Uniprot:Q8IVF2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 6.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_138420.4	NP_612429.2	7	yes	-
ENST00000333244.6	ENSP00000353114.4	7	yes	-
NM_001350929.2	NP_001337858.1	4	-	-
ENST00000557457.1	ENSP00000450998.1	1	-	-

Phenotypes

GenCC

Source: genCC

• Charcot-Marie-Tooth disease (Limited), mode of inheritance: AR
• Charcot-Marie-Tooth disease (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AHNAK2 gene.

• not_specified (1773 variants)
• not_provided (448 variants)
• AHNAK2-related_disorder (5 variants)
• Abnormality_of_neuronal_migration (2 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
• Dysmetria (1 variants)
• Migraine (1 variants)
• Enhancement_of_the_C-reflex (1 variants)
• Hereditary_episodic_ataxia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AHNAK2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_138420.4. 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			9	210	29	248
missense			1502	358	45	1905
nonsense			1			1
start loss						0
frameshift			2	1	3	6
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	1515	569	77

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AHNAK2	protein_coding	protein_coding	ENST00000333244	7	41114

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124612	0	20	124632	0.0000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-12.2	5006	3.09e+3	1.62	0.000185	37051
Missense in Polyphen		1197	758.67	1.5778		9817
Synonymous	-22.2	2382	1.35e+3	1.77	0.0000985	11684
Loss of Function	1.54	7	13.0	0.538	7.01e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000117	0.000117
Ashkenazi Jewish	0.0000997	0.0000994
East Asian	0.0000556	0.0000556
Finnish	0.0000497	0.0000464
European (Non-Finnish)	0.0000818	0.0000796
Middle Eastern	0.0000556	0.0000556
South Asian	0.000134	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.908
• rvis_EVS: 27.6
• rvis_percentile_EVS: 99.99

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0502

Gene Damage Prediction

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

Gene ontology

• Biological process: plasma membrane repair;regulation of RNA splicing
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane;Z disc;T-tubule;cytoplasmic vesicle membrane;sarcolemma;costamere
• Molecular function: protein binding