SRM

spermidine synthase, the group of Seven-beta-strand methyltransferase motif containing

Basic information

Region (hg38): 1:11054584-11060020

Previous symbols: [ "SRML1" ]

Links

ENSG00000116649

∙ NCBI:6723 ∙ OMIM:182891 ∙ HGNC:11296 ∙ Uniprot:P19623 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRM 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						0
missense			10 clinvar	1 clinvar		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in SRM

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

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

Position	Phenotype	Significance	ClinVar
1-11054876-C-A	not specified	Uncertain significance (Jan 26, 2023)	2479369
1-11054964-T-C	not specified	Uncertain significance (Sep 25, 2024)	3449354
1-11054997-G-A	not specified	Uncertain significance (Dec 11, 2024)	3801382
1-11055006-C-T	not specified	Uncertain significance (Sep 16, 2021)	3170003
1-11055036-C-T	not specified	Uncertain significance (Oct 12, 2024)	3449356
1-11055069-C-T	not specified	Uncertain significance (Jul 14, 2021)	2232079
1-11055071-T-C	not specified	Likely benign (Jul 13, 2022)	2301517
1-11055080-G-A	not specified	Uncertain significance (Dec 24, 2024)	3801383
1-11056037-T-C	not specified	Uncertain significance (Jan 23, 2024)	3170002
1-11058813-C-T	not specified	Uncertain significance (Feb 02, 2022)	2275224
1-11059263-C-A	not specified	Uncertain significance (Jan 10, 2025)	3801380
1-11059823-G-T	not specified	Uncertain significance (Oct 03, 2024)	3449355
1-11059900-G-A	not specified	Uncertain significance (Oct 30, 2023)	3170001
1-11059906-G-A	not specified	Uncertain significance (Jul 27, 2022)	2303956

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRM	protein_coding	protein_coding	ENST00000376957	8	5441

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.235	0.764	125620	0	7	125627	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.55	81	176	0.459	0.0000101	1958
Missense in Polyphen		11	65.46	0.16804		713
Synonymous	-0.409	82	77.4	1.06	0.00000498	565
Loss of Function	2.78	4	16.0	0.249	6.84e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000301	0.0000301
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000361	0.0000352
Middle Eastern	0.0000548	0.0000544
South Asian	0.0000336	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM). Has a strong preference for putrescine as substrate, and has very low activity towards 1,3-diaminopropane. Has extremely low activity towards spermidine. {ECO:0000269|PubMed:17585781}.;
Pathway: Arginine and proline metabolism - Homo sapiens (human);beta-Alanine metabolism - Homo sapiens (human);Glutathione metabolism - Homo sapiens (human);Cysteine and methionine metabolism - Homo sapiens (human);S-Adenosylhomocysteine (SAH) Hydrolase Deficiency;Methionine Metabolism;Methionine Adenosyltransferase Deficiency;Glycine N-methyltransferase Deficiency;Hypermethioninemia;Methylenetetrahydrofolate Reductase Deficiency (MTHFRD);Homocystinuria-megaloblastic anemia due to defect in cobalamin metabolism, cblG complementation type;Spermidine and Spermine Biosynthesis;Cystathionine Beta-Synthase Deficiency;Methionine De Novo and Salvage Pathway;Amino Acid metabolism;Nucleotide Metabolism;Urea cycle and metabolism of amino groups;Metabolism of polyamines;Metabolism of amino acids and derivatives;Metabolism;Arginine Proline metabolism;spermidine biosynthesis;methionine salvage cycle III (Consensus)

Recessive Scores

pRec: 0.291

Intolerance Scores

loftool: 0.268
rvis_EVS: -0.38
rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

pHI: 0.188
hipred: Y
hipred_score: 0.728
ghis: 0.594

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Srm
Phenotype

Zebrafish Information Network

Gene name: srm
Affected structure: melanophore stripe
Phenotype tag: abnormal
Phenotype quality: patchy

Gene ontology

Biological process: polyamine metabolic process;polyamine biosynthetic process;spermidine biosynthetic process;cellular response to leukemia inhibitory factor
Cellular component: cytosol
Molecular function: spermidine synthase activity;protein binding;identical protein binding;protein homodimerization activity