AHSG

alpha 2-HS glycoprotein, the group of Cystatins, type 4

Basic information

Region (hg38): 3:186613060-186621318

Links

ENSG00000145192

∙ NCBI:197 ∙ OMIM:138680 ∙ HGNC:349 ∙ Uniprot:P02765 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

alopecia-intellectual disability syndrome 1 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Alopecia-intellectual disability syndrome 1	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic; Neurologic	28054173

ClinVar

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

not_specified (49 variants)
not_provided (13 variants)
Alopecia-intellectual_disability_syndrome_1 (3 variants)
AHSG-related_disorder (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AHSG gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001622.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar	2 clinvar	6
missense	1 clinvar		44 clinvar	5 clinvar	5 clinvar	55
nonsense		1 clinvar				1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	1	44	9	7

Highest pathogenic variant AF is 0.0000941847

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AHSG	protein_coding	protein_coding	ENST00000411641	7	8396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.21e-10	0.0477	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.364	223	208	1.07	0.0000108	2342
Missense in Polyphen		70	62.872	1.1134		734
Synonymous	1.17	74	88.0	0.841	0.00000511	784
Loss of Function	-0.266	14	13.0	1.08	5.49e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.000796	0.000794
East Asian	0.000110	0.000109
Finnish	0.000832	0.000832
European (Non-Finnish)	0.000291	0.000290
Middle Eastern	0.000110	0.000109
South Asian	0.0000653	0.0000653
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: Promotes endocytosis, possesses opsonic properties and influences the mineral phase of bone. Shows affinity for calcium and barium ions.;
Disease: DISEASE: Alopecia-mental retardation syndrome 1 (APMR1) [MIM:203650]: A rare autosomal recessive form of alopecia. APMR1 patients show loss of hair on the scalp, absence of eyebrows, eyelashes, axillary and pubic hair, and mild to severe mental retardation. {ECO:0000269|PubMed:28054173}. Note=The disease may be caused by mutations affecting the gene represented in this entry.;
Pathway: Neutrophil degranulation;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;BMP receptor signaling;Hemostasis (Consensus)

Recessive Scores

pRec: 0.392

Intolerance Scores

loftool: 0.846
rvis_EVS: 0.69
rvis_percentile_EVS: 85.18

Haploinsufficiency Scores

pHI: 0.472
hipred: N
hipred_score: 0.123
ghis: 0.601

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.596

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ahsg
Phenotype: growth/size/body region phenotype; muscle phenotype; homeostasis/metabolism phenotype; skeleton phenotype; hearing/vestibular/ear phenotype; limbs/digits/tail phenotype;

Gene ontology

Biological process: skeletal system development;ossification;platelet degranulation;pinocytosis;acute-phase response;negative regulation of endopeptidase activity;regulation of bone mineralization;negative regulation of bone mineralization;negative regulation of kinase activity;neutrophil degranulation;post-translational protein modification;cellular protein metabolic process;negative regulation of insulin receptor signaling pathway;regulation of inflammatory response;positive regulation of phagocytosis
Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen;Golgi apparatus;platelet alpha granule lumen;secretory granule lumen;collagen-containing extracellular matrix;extracellular exosome;blood microparticle
Molecular function: cysteine-type endopeptidase inhibitor activity;kinase inhibitor activity