MAP6D1

MAP6 domain containing 1

Basic information

Region (hg38): 3:183815922-183825594

Links

ENSG00000180834 ∙ NCBI:79929 ∙ OMIM:610593 ∙ HGNC:25753 ∙ Uniprot:Q9H9H5 ∙ 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 MAP6D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP6D1 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				1	1	2
missense			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	13	2	1

Variants in MAP6D1

This is a list of pathogenic ClinVar variants found in the MAP6D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-183817373-G-A		not specified	Uncertain significance (Dec 08, 2023)
3-183817434-G-A		MAP6D1-related disorder	Likely benign (Aug 26, 2019)
3-183818091-G-T		not specified	Uncertain significance (Aug 15, 2023)
3-183818100-T-C		not specified	Uncertain significance (Feb 23, 2023)
3-183825180-G-A		not specified	Uncertain significance (Aug 13, 2021)
3-183825187-C-T		not specified	Uncertain significance (Mar 19, 2024)
3-183825192-G-C		not specified	Uncertain significance (Feb 23, 2023)
3-183825205-C-T		not specified	Uncertain significance (Apr 27, 2022)
3-183825220-G-T		not specified	Uncertain significance (Jul 20, 2022)
3-183825243-G-A		not specified	Likely benign (Sep 20, 2023)
3-183825244-C-T		MAP6D1-related disorder	Benign (Jul 10, 2024)
3-183825280-C-T		not specified	Uncertain significance (May 12, 2024)
3-183825287-C-T		MAP6D1-related disorder	Likely benign (Aug 29, 2022)
3-183825311-G-A		MAP6D1-related disorder	Benign (Aug 21, 2019)
3-183825379-C-A		not specified	Uncertain significance (May 11, 2022)
3-183825391-G-T		not specified	Uncertain significance (Jan 26, 2022)
3-183825403-G-A		not specified	Uncertain significance (Dec 15, 2021)
3-183825417-C-T		not specified	Uncertain significance (Apr 05, 2023)
3-183825462-G-A		not specified	Uncertain significance (Jan 26, 2023)
3-183825516-C-A		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP6D1	protein_coding	protein_coding	ENST00000318631	3	9719

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.110	0.787	125724	0	6	125730	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.175	59	55.3	1.07	0.00000297	1162
Missense in Polyphen		19	20.697	0.918		465
Synonymous	0.570	20	23.5	0.850	0.00000138	429
Loss of Function	1.28	2	5.12	0.391	3.05e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have microtubule-stabilizing activity. {ECO:0000250}.

Recessive Scores

• pRec: 0.0872

Haploinsufficiency Scores

• pHI: 0.0721
• hipred: N
• hipred_score: 0.146
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0169

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map6d1

Gene ontology

• Biological process: microtubule cytoskeleton organization;negative regulation of microtubule depolymerization;N-terminal peptidyl-L-cysteine N-palmitoylation;cytoskeleton-dependent intracellular transport;regulation of microtubule cytoskeleton organization
• Cellular component: Golgi-associated vesicle;cis-Golgi network;microtubule
• Molecular function: calmodulin binding;microtubule binding