Is PUS7 p.Ser55= (c.165T>C) pathogenic?

PUS7 p.Ser55= (c.165T>C) is classified Likely benign in PUS7 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-19). Ultra-rare (popmax 0.0986%, afr); Associated with PUS7-related disorder.

What condition is associated with PUS7 p.Ser55= (c.165T>C)?

PUS7 p.Ser55= (c.165T>C) is associated with PUS7-related disorder (ClinVar).

How common is PUS7 p.Ser55= (c.165T>C) in the general population?

PUS7 p.Ser55= (c.165T>C) is ultra-rare (popmax 0.0986%, afr) (gnomAD).

PUS7 p.Ser55=

c.165T>C · rs145057276 · VCV3040846

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0986%, afr)

Conditions

PUS7-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.27	GERP -1.8
Overall
CADD	1.109	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0986% African / African-American · 74/75,016 alleles

Filtering AF 0.0805% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0739%

Overall 0.00458% 74/1,614,080 alleles · ultra-rare exomes 36/1,461,892 · genomes 38/152,188 · joint denominator

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: PUS7
Protein: p.Ser55=
Coding: c.165T>C
MANE Select: NM_019042
dbSNP: rs145057276
Type: single nucleotide variant
Location: chr7:105508348 (GRCh38)
Gene constraint: LOEUF 0.727 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.67 · 1 PDB
Residue 55: the 'disordered' region

Full PUS7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

PUS7-related disorder

Similar variants

PUS7 c.*5T>C Benign same condition
PUS7 p.Ala272= Likely benign same condition
PUS7 p.His123Tyr Benign same condition
PUS7 p.Leu438= Benign same condition
PUS7 c.921-5dup Benign same condition
PUS7 c.921-6_921-5del Likely benign same condition
PUS7 c.921-7_921-5del Likely benign same condition
PUS7 c.1399-1G>C Pathogenic/Likely pathogenic ★★ 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/pus7-p-ser55 (accessed [today's date]).

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