Is PSPH p.Gly53= (c.159C>T) pathogenic?

PSPH p.Gly53= (c.159C>T) is classified Benign in PSPH (ClinVar, Multiple submitters, 3 submitters; last evaluated 2021-03-31). Common (popmax 42.7%, afr) — too common for a highly-penetrant pathogenic allele; Associated with PSPH deficiency.

What condition is associated with PSPH p.Gly53= (c.159C>T)?

PSPH p.Gly53= (c.159C>T) is associated with PSPH deficiency (ClinVar).

PSPH p.Gly53=

Q: How common is PSPH p.Gly53= (c.159C>T) in the general population?

PSPH p.Gly53= (c.159C>T) is common (popmax 42.7%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.159C>T · rs74874687 · VCV360507

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 42.7%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

PSPH deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -7.6	GERP -5.1
Overall
CADD	2.771	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 42.7% African / African-American · 24,556/57,456 alleles

Filtering AF 42.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 42.1%

Overall 7.02% 90,508/1,289,266 alleles · common exomes 52,550/1,146,796 · genomes 37,958/142,470 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	42.7%	2
East Asian	36.2%	3
Admixed American	16.6%	6
South Asian	15.6%	6
Finnishnot grpmax-eligible	13%	8
Middle Eastern	11.1%	9
Amishnot grpmax-eligible	8.03%	12
Remaining individualsnot grpmax-eligible	6.7%	15
Ashkenazi Jewishnot grpmax-eligible	4.63%	22
European (non-Finnish)	2.98%	34

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: PSPH
Protein: p.Gly53=
Coding: c.159C>T
MANE Select: NM_004577
dbSNP: rs74874687
Type: single nucleotide variant
Location: chr7:56019716 (GRCh38)
Gene constraint: LOEUF 1.063 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 92.88 · 6 PDB
Residue 53: a turn; a binding site

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

Disease context

PSPH deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PSPH p.Arg101Ter Likely pathogenic ★★ same condition
PSPH c.422-3A>C Uncertain significance ★★ same condition
PSPH c.570+3A>G Uncertain significance ★★ same condition
PSPH c.570+5G>C Uncertain significance ★★ same condition
PSPH c.*341G>A Uncertain significance ★★ same condition
PSPH p.Asn124Ser Uncertain significance ★★ ⚠ same condition
PSPH p.Asp32Asn Uncertain significance ★★ ⚠ same condition
PSPH p.Gln204His 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/psph-p-gly53 (accessed [today's date]).

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