Is MAP4 p.Asp16= (c.48C>T) pathogenic?

MAP4 p.Asp16= (c.48C>T) is classified Likely benign in MAP4 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-24). Ultra-rare (popmax 0.0833%, amr); Associated with MAP4-related disorder.

What condition is associated with MAP4 p.Asp16= (c.48C>T)?

MAP4 p.Asp16= (c.48C>T) is associated with MAP4-related disorder (ClinVar).

How common is MAP4 p.Asp16= (c.48C>T) in the general population?

MAP4 p.Asp16= (c.48C>T) is ultra-rare (popmax 0.0833%, amr) (gnomAD).

MAP4 p.Asp16=

c.48C>T · rs375224658 · VCV3043664

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0833%, amr)

Conditions

MAP4-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.094	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.29	GERP -0.62, phastCons 1
Overall
CADD	6.708	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0833% Admixed American · 50/59,996 alleles

Filtering AF 0.0649% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0584%

Overall 0.0173% 279/1,614,008 alleles · ultra-rare exomes 257/1,461,852 · genomes 22/152,156 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0833%	1,200
European (non-Finnish)	0.0181%	5,514
Middle Eastern	0.0164%	6,084
Remaining individualsnot grpmax-eligible	0.016%	6,248
African / African-American	0.00534%	18,726

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.Asp16=
Coding: c.48C>T
MANE Select: NM_001385682
dbSNP: rs375224658
Type: single nucleotide variant
Location: chr3:47998813 (GRCh38)
Gene constraint: LOEUF 0.512 · pLI 0.14 (gnomAD)
Structure: AlphaFold pLDDT 43.03

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

Disease context

MAP4-related disorder

Similar variants

MAP4 c.292+2409G>A Likely benign same condition
MAP4 c.*100G>A Likely benign same condition
MAP4 c.*44G>A Likely benign same condition
MAP4 p.Ala2123= Likely benign same condition
MAP4 p.Ala2134= Likely benign same condition
MAP4 p.Ala437= Likely benign same condition
MAP4 p.Arg23Gln Benign same condition
MAP4 p.Arg23Trp Likely benign ⚠ 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/map4-p-asp16 (accessed [today's date]).

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