Is MAP1B p.Ala796Thr (c.2386G>A) pathogenic?

MAP1B p.Ala796Thr (c.2386G>A) is classified Benign in MAP1B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-27). AlphaMissense: likely benign (0.0802); Low-frequency (popmax 2.23%, nfe); Associated with MAP1B-related disorder.

What condition is associated with MAP1B p.Ala796Thr (c.2386G>A)?

MAP1B p.Ala796Thr (c.2386G>A) is associated with MAP1B-related disorder (ClinVar).

How common is MAP1B p.Ala796Thr (c.2386G>A) in the general population?

MAP1B p.Ala796Thr (c.2386G>A) is low-frequency (popmax 2.23%, nfe) (gnomAD).

What do computational predictors say about MAP1B p.Ala796Thr (c.2386G>A)?

AlphaMissense predicts likely benign (score 0.0802) — an in-silico prediction, not a clinical call.

MAP1B p.Ala796Thr

c.2386G>A · rs35473133 · VCV3038000

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0802 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.23%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

MAP1B-related disorder

Computational evidence

Protein change
AlphaMissense	0.0802	likely benign
REVEL	0.072	moderately benign-leaning
SaProt	LLR -8.04	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.7	GERP 0.8, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 5,330 bp · p 1.3e-05 · regional, not allelic
Overall
CADD	17.12	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.23% European (non-Finnish) · 26,328/1,180,048 alleles

Filtering AF 2.21% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.2%

Overall 1.79% 28,955/1,614,236 alleles · low-frequency exomes 27,006/1,461,890 · genomes 1,949/152,346 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	2.23%	45
Remaining individualsnot grpmax-eligible	1.41%	71
Admixed American	0.921%	109
Finnishnot grpmax-eligible	0.809%	124
Ashkenazi Jewishnot grpmax-eligible	0.567%	176
African / African-American	0.408%	245
Middle Eastern	0.247%	404
South Asian	0.202%	495

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.Ala796Thr
Coding: c.2386G>A
MANE Select: NM_005909
dbSNP: rs35473133
Type: single nucleotide variant
Location: chr5:72195741 (GRCh38)
Gene constraint: LOEUF 0.105 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 46.18
Residue 796: a UniProt-annotated variant site (in pvnh9)

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

Disease context

MAP1B-related disorder

Similar variants

MAP1B p.Ala796Val Benign ★★ same residue
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

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-ala796thr (accessed [today's date]).

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