Is LITAF p.Asp143= (c.429C>T) pathogenic?

LITAF p.Asp143= (c.429C>T) is classified Likely benign in LITAF (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-05-21). Ultra-rare (popmax 0.0267%, amr); Associated with Charcot-Marie-Tooth disease type 1C.

What condition is associated with LITAF p.Asp143= (c.429C>T)?

LITAF p.Asp143= (c.429C>T) is associated with Charcot-Marie-Tooth disease type 1C (ClinVar).

How common is LITAF p.Asp143= (c.429C>T) in the general population?

LITAF p.Asp143= (c.429C>T) is ultra-rare (popmax 0.0267%, amr) (gnomAD).

How is Charcot-Marie-Tooth disease type 1C inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

LITAF p.Asp143=

c.429C>T · rs374918259 · VCV2912264

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0267%, amr)

Conditions

Charcot-Marie-Tooth disease type 1C

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.253	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.3	GERP -4.2
Overall
CADD	9.047	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0267% Admixed American · 16/59,972 alleles

Filtering AF 0.0166% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0136%

Overall 0.0026% 42/1,613,750 alleles · ultra-rare exomes 26/1,461,470 · genomes 16/152,280 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0267%	3,748
Remaining individualsnot grpmax-eligible	0.0176%	5,681
African / African-American	0.008%	12,504
South Asian	0.0022%	45,484
European (non-Finnish)	0.000593%	168,552

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: LITAF
Protein: p.Asp143=
Coding: c.429C>T
MANE Select: NM_001136472
dbSNP: rs374918259
Type: single nucleotide variant
Location: chr16:11549694 (GRCh38)
Gene constraint: LOEUF 1.017 · pLI 0.02 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 70.60
Residue 143: the litaf domain

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

Disease context

Charcot-Marie-Tooth disease type 1C — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Charcot-Marie-Tooth disease type 1C (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood
Prevalence: <1 / 1 000 000 (Europe)

Similar variants

LITAF p.Asp143Glu Uncertain significance ★★ ⚠ same residue
LITAF p.Asp143Tyr Uncertain significance ★ ⚠ same residue
LITAF p.Ala111Gly Pathogenic ★★ same condition
LITAF p.Gly112Ser Pathogenic ★★ ⚠ same condition
LITAF p.Thr115Asn Pathogenic/Likely pathogenic ★★ same condition
LITAF c.220+4C>T Uncertain significance ★★ same condition
LITAF p.Ala129Val Uncertain significance ★★ ⚠ same condition
LITAF p.Ala140Thr 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/litaf-p-asp143 (accessed [today's date]).

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