Is TIMP3 p.Phe120= (c.360C>T) pathogenic?

TIMP3 p.Phe120= (c.360C>T) is classified Benign/Likely benign in TIMP3 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-10-05). Rare (popmax 0.35%, sas).

How common is TIMP3 p.Phe120= (c.360C>T) in the general population?

TIMP3 p.Phe120= (c.360C>T) is rare (popmax 0.35%, sas) (gnomAD).

TIMP3 p.Phe120=

c.360C>T · rs563656481 · VCV1170518

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.35%, sas)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -11	GERP -6.6
Overall
CADD	4.942	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.35% South Asian · 319/91,076 alleles

Filtering AF 0.319% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.306%

Overall 0.0218% 352/1,614,156 alleles · rare exomes 325/1,461,890 · genomes 27/152,266 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.35%	286
Remaining individualsnot grpmax-eligible	0.0176%	5,683
Middle Eastern	0.0165%	6,062
African / African-American	0.0107%	9,382
European (non-Finnish)	0.0011%	90,771

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: TIMP3
Protein: p.Phe120=
Coding: c.360C>T
MANE Select: NM_000362
dbSNP: rs563656481
Type: single nucleotide variant
Location: chr22:32858060 (GRCh38)

Full TIMP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/timp3-p-phe120 (accessed [today's date]).

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