Is MAP1B p.Gly286= (c.858C>T) pathogenic?

MAP1B p.Gly286= (c.858C>T) is classified Likely benign in MAP1B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-25). Ultra-rare (popmax 0.024%, afr); Associated with MAP1B-related disorder.

What condition is associated with MAP1B p.Gly286= (c.858C>T)?

MAP1B p.Gly286= (c.858C>T) is associated with MAP1B-related disorder (ClinVar).

How common is MAP1B p.Gly286= (c.858C>T) in the general population?

MAP1B p.Gly286= (c.858C>T) is ultra-rare (popmax 0.024%, afr) (gnomAD).

MAP1B p.Gly286=

c.858C>T · rs777817448 · VCV3035516

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.024%, afr)

Conditions

MAP1B-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.87	GERP -3.5, phastCons 0.98
Overall
CADD	8.641	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.024% African / African-American · 18/74,904 alleles

Filtering AF 0.0155% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0128%

Overall 0.00415% 67/1,614,018 alleles · ultra-rare exomes 50/1,461,892 · genomes 17/152,126 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.024%	4,161
Finnishnot grpmax-eligible	0.0125%	8,003
Remaining individualsnot grpmax-eligible	0.0064%	15,622
South Asian	0.00329%	30,357
European (non-Finnish)	0.0028%	35,758
East Asian	0.00223%	44,900

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MAP1B
Protein: p.Gly286=
Coding: c.858C>T
MANE Select: NM_005909
dbSNP: rs777817448
Type: single nucleotide variant
Location: chr5:72194213 (GRCh38)
Gene constraint: LOEUF 0.105 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 46.18

Full MAP1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MAP1B-related disorder

Similar variants

MAP1B p.Pro1182Arg Uncertain significance ★★ ⚠ same condition
MAP1B p.Thr2194Met Uncertain significance ★★ ⚠ same condition
MAP1B p.Gln325Ter Likely pathogenic ★ same condition
MAP1B p.Lys751Ter Likely pathogenic ★ same condition
MAP1B p.Arg64Gln Uncertain significance ★ same condition
MAP1B p.Asp1637Asn Uncertain significance ★ ⚠ same condition
MAP1B p.Glu678Gly Uncertain significance ★ ⚠ same condition
MAP1B p.Glu927Asp Uncertain significance ★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/map1b-p-gly286 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown