AMH

anti-Mullerian hormone, the group of MicroRNA protein coding host genes|Receptor ligands|Transforming growth factor beta superfamily

Basic information

Region (hg38): 19:2249309-2252073

Links

ENSG00000104899 ∙ NCBI:268 ∙ OMIM:600957 ∙ HGNC:464 ∙ Uniprot:P03971 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• persistent Mullerian duct syndrome (Supportive), mode of inheritance: AR
• persistent Mullerian duct syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Persistent Mullerian duct syndrome, type I	AR	Endocrine; Oncologic; Genitourinary	In males, recognition can allow surveillance and surgical explorations to correct manifestations such as cryptorchdisim, which can be important to preserve fertility and decrease the chance of related sequelae (eg, testicular tumors)	Endocrine; Genitourinary; Oncologic	8872466; 8895659; 11760020; 15878900; 18547961; 22188863

ClinVar

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

• not provided (4 variants)
• Persistent Mullerian duct syndrome (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMH gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				32	7	39
missense	1	2	68	10	5	86
nonsense	3					3
start loss						0
frameshift	2					2
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region				1	1	2
non coding				3	5	8
Total	7	2	68	45	17

Highest pathogenic variant AF is 0.0000855

Variants in AMH

This is a list of pathogenic ClinVar variants found in the AMH region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-2249331-C-T		AMH-related disorder	Likely benign (Aug 12, 2024)
19-2249337-G-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Feb 28, 2023)
19-2249355-G-C			Uncertain significance (Dec 01, 2023)
19-2249357-C-A		Inborn genetic diseases	Uncertain significance (Nov 22, 2022)
19-2249367-T-G		AMH-related disorder	Uncertain significance (Oct 14, 2024)
19-2249384-G-A		Inborn genetic diseases	Uncertain significance (Dec 05, 2022)
19-2249385-C-T			Likely benign (Nov 27, 2023)
19-2249408-A-G			Uncertain significance (Sep 24, 2021)
19-2249423-G-T		Inborn genetic diseases	Uncertain significance (May 13, 2024)
19-2249460-T-C		Inborn genetic diseases	Uncertain significance (Aug 26, 2022)
19-2249461-G-A			Likely benign (Jan 12, 2024)
19-2249468-C-G		not specified	Uncertain significance (Jun 01, 2024)
19-2249469-C-A		Inborn genetic diseases	Uncertain significance (Dec 14, 2023)
19-2249478-G-T		Persistent Mullerian duct syndrome	Benign (Jan 31, 2024)
19-2249482-AC-A		Persistent Mullerian duct syndrome	Pathogenic (Dec 22, 2019)
19-2249498-C-T			Likely benign (Oct 03, 2023)
19-2249506-A-G		not specified	Likely benign (May 22, 2019)
19-2249512-C-T			Likely benign (Apr 23, 2023)
19-2249534-T-TC			Pathogenic (Mar 14, 2024)
19-2249559-T-C			Uncertain significance (Dec 01, 2023)
19-2249564-G-A			Uncertain significance (Feb 24, 2022)
19-2249583-T-A			Uncertain significance (Nov 16, 2021)
19-2249583-T-C		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)
19-2249584-G-A			Benign (Jan 29, 2024)
19-2249605-C-T		AMH-related disorder	Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMH	protein_coding	protein_coding	ENST00000221496	5	2765

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.40e-12	0.0123	124927	0	39	124966	0.000156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.881	336	294	1.14	0.0000194	3296
Missense in Polyphen		143	124.41	1.1495		1462
Synonymous	-1.32	163	143	1.14	0.00000982	1330
Loss of Function	-0.701	16	13.2	1.21	7.45e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000778	0.000592
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.000192	0.000185
European (Non-Finnish)	0.000148	0.000133
Middle Eastern	0.000112	0.000109
South Asian	0.000102	0.0000980
Other	0.000342	0.000328

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This glycoprotein, produced by the Sertoli cells of the testis, causes regression of the Muellerian duct. It is also able to inhibit the growth of tumors derived from tissues of Muellerian duct origin.
• Disease: DISEASE: Persistent Muellerian duct syndrome 1 (PMDS1) [MIM:261550]: A form of male pseudohermaphroditism characterized by a failure of Muellerian duct regression in otherwise normal males. {ECO:0000269|PubMed:8162013, ECO:0000269|PubMed:8872466}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: TGF-beta signaling pathway - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);TGF-Core;Mesodermal Commitment Pathway;Signal Transduction;Signaling by BMP;Signaling by TGF-beta family members;ALK2 signaling events (Consensus)

Haploinsufficiency Scores

• pHI: 0.346
• hipred: N
• hipred_score: 0.220
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.768

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Amh
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; reproductive system phenotype; neoplasm

Zebrafish Information Network

• Gene name: amh
• Affected structure: spermatogonium
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: preantral ovarian follicle growth;urogenital system development;Mullerian duct regression;cell-cell signaling;gonadal mesoderm development;sex determination;sex differentiation;aging;regulation of signaling receptor activity;positive regulation of gene expression;response to organic cyclic compound;BMP signaling pathway;response to drug;positive regulation of NF-kappaB transcription factor activity;negative regulation of ovarian follicle development
• Cellular component: extracellular region;extracellular space
• Molecular function: signaling receptor binding;transforming growth factor beta receptor binding;hormone activity;growth factor activity