Is TERF2IP p.Pro59Arg (c.176C>G) pathogenic?

TERF2IP p.Pro59Arg (c.176C>G) is classified Uncertain significance in TERF2IP (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-04). AlphaMissense: ambiguous (0.5172); Very rare (popmax 0.00111%, sas).

How common is TERF2IP p.Pro59Arg (c.176C>G) in the general population?

TERF2IP p.Pro59Arg (c.176C>G) is very rare (popmax 0.00111%, sas) (gnomAD).

What do computational predictors say about TERF2IP p.Pro59Arg (c.176C>G)?

AlphaMissense predicts ambiguous (score 0.5172) — an in-silico prediction, not a clinical call.

TERF2IP p.Pro59Arg

c.176C>G · rs2082314277 · VCV1779758

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5172 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00111%, sas)

Computational evidence

Protein change
AlphaMissense	0.5172	ambiguous
REVEL	0.322	indeterminate
SaProt	LLR -6.38	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.9, phastCons 1
Regional constraint	o/e 1.11	unconstrained · MANE · 8,725 bp · p 0.011 · regional, not allelic
Overall
CADD	28.4	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 0.00111% South Asian · 1/89,834 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000188% 3/1,595,814 alleles · very rare exomes 2/1,443,718 · genomes 1/152,096 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00111%	89,834
European (non-Finnish)	0.000171%	585,700

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: TERF2IP
Protein: p.Pro59Arg
Coding: c.176C>G
MANE Select: NM_018975
dbSNP: rs2082314277
Type: single nucleotide variant
Location: chr16:75648058 (GRCh38)
Gene constraint: LOEUF 1.45 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.76 · 5 PDB

Full TERF2IP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TERF2IP p.Pro59Ser Uncertain significance ★★ ⚠ same residue
TERF2IP p.Pro59= Likely benign ★★ same residue
TERF2IP p.Ala123Gly Uncertain significance ★★ ⚠ same type
TERF2IP p.Ala200Gly Uncertain significance ★★ ⚠ same type
TERF2IP p.Ala387Val Uncertain significance ★★ ⚠ same type
TERF2IP p.Ala61Thr Uncertain significance ★★ ⚠ same type
TERF2IP p.Ala65Thr Uncertain significance ★★ ⚠ same type
TERF2IP p.Arg133Gln 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/terf2ip-p-pro59arg (accessed [today's date]).

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