Is MAP4 p.Pro488Leu (c.1463C>T) pathogenic?

MAP4 p.Pro488Leu (c.1463C>T) is classified Likely benign in MAP4 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-06). AlphaMissense: likely benign (0.0545); Ultra-rare (popmax 0.0262%, nfe).

How common is MAP4 p.Pro488Leu (c.1463C>T) in the general population?

MAP4 p.Pro488Leu (c.1463C>T) is ultra-rare (popmax 0.0262%, nfe) (gnomAD).

What do computational predictors say about MAP4 p.Pro488Leu (c.1463C>T)?

AlphaMissense predicts likely benign (score 0.0545) — an in-silico prediction, not a clinical call.

MAP4 p.Pro488Leu

c.1463C>T · rs139367836 · VCV2368136

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0545 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0262%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0545	likely benign
REVEL	0.009	strongly benign-leaning
SaProt	LLR -6.18	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 -2.1	GERP -3.3
Regional constraint	o/e 0.91	unconstrained · MANE · 123 kb · p 2.5e-05 · regional, not allelic
Overall
CADD	0.017	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 0.0262% European (non-Finnish) · 309/1,180,038 alleles

Filtering AF 0.0237% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0228%

Overall 0.0203% 328/1,614,024 alleles · ultra-rare exomes 318/1,461,888 · genomes 10/152,136 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0262%	3,819
Remaining individualsnot grpmax-eligible	0.0096%	10,414
Finnishnot grpmax-eligible	0.00937%	10,672
African / African-American	0.00401%	24,963
Admixed American	0.00333%	29,998
East Asian	0.00223%	44,898
South Asian	0.0011%	91,082

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: MAP4
Protein: p.Pro488Leu
Coding: c.1463C>T
MANE Select: NM_001385682
dbSNP: rs139367836
Type: single nucleotide variant
Location: chr3:47916364 (GRCh38)
Gene constraint: LOEUF 0.512 · pLI 0.14 (gnomAD)
Structure: AlphaFold pLDDT 43.03
Residue 488: the '17 x 14 aa tandem repeats' region

Full MAP4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MAP4 c.292+9T>G Benign ★★ same type
MAP4 p.Gln1950= Benign ★★ same type
MAP4 p.Leu516= Likely benign ★★ same type
MAP4 p.Val37= Benign ★★ same type
MAP4 p.Ala150Ser Uncertain significance ★ ⚠ same type
MAP4 p.Ala1922Val Uncertain significance ★ ⚠ same type
MAP4 p.Ala1926Pro Uncertain significance ★ ⚠ same type
MAP4 p.Ala1941Thr Uncertain significance ★ ⚠ same type

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/map4-p-pro488leu (accessed [today's date]).

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