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.

• not_specified (33 variants)
• MAP6D1-related_disorder (4 variants)

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. These statistics are base on transcript: NM_000024871.4. 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				2	1	3
missense			32	1	1	34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	3	2

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