Is MAP1B p.Lys710Arg (c.2129A>G) pathogenic?

MAP1B p.Lys710Arg (c.2129A>G) is classified Benign in MAP1B (ClinVar, Single submitter, 3 submitters; last evaluated 2018-12-03). AlphaMissense: likely benign (0.1077); Rare (popmax 0.924%, afr).

How common is MAP1B p.Lys710Arg (c.2129A>G) in the general population?

MAP1B p.Lys710Arg (c.2129A>G) is rare (popmax 0.924%, afr) (gnomAD).

What do computational predictors say about MAP1B p.Lys710Arg (c.2129A>G)?

AlphaMissense predicts likely benign (score 0.1077) — an in-silico prediction, not a clinical call.

MAP1B p.Lys710Arg

c.2129A>G · rs138733653 · VCV712572

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1077 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.924%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1077	likely benign
REVEL	0.096	moderately benign-leaning
SaProt	LLR -10.34	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.1	GERP 1.2, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 5,330 bp · p 1.3e-05 · regional, not allelic
Overall
CADD	19.72	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 0.924% African / African-American · 675/73,044 alleles

Filtering AF 0.866% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.843%

Overall 0.0466% 740/1,588,886 alleles · rare exomes 344/1,436,734 · genomes 396/152,152 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.924%	108
Remaining individualsnot grpmax-eligible	0.0538%	1,860
Admixed American	0.0508%	1,967
Middle Eastern	0.017%	5,876
European (non-Finnish)	0.000341%	293,308

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.Lys710Arg
Coding: c.2129A>G
MANE Select: NM_005909
dbSNP: rs138733653
Type: single nucleotide variant
Location: chr5:72195484 (GRCh38)
Gene constraint: LOEUF 0.105 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 46.18
Residue 710: the 'disordered' region; a UniProt-annotated variant site (in pvnh9)

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

Similar variants

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MAP1B p.Arg85Ter Pathogenic/Likely pathogenic ★★ same type
MAP1B p.Arg999Ter Pathogenic/Likely pathogenic ★★ same type
MAP1B p.Ala966Val Uncertain significance ★★ ⚠ same type
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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-lys710arg (accessed [today's date]).

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